Constitutive and numerical modeling of soil and soil-pile interaction for 3D applications and Kealakaha stream bridge case study.

DOT National Transportation Integrated Search

2011-12-01

This study is concerned with developing new modeling tools for predicting the response of the new Kealakaha : Stream Bridge to static and dynamic loads, including seismic shaking. The bridge will span 220 meters, with the : deck structure being curve...

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

75 FR 16202 - Office of New Reactors; Interim Staff Guidance on Ensuring Hazard-Consistent Seismic Input for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-31

... Staff Guidance on Ensuring Hazard-Consistent Seismic Input for Site Response and Soil Structure...-Consistent Seismic Input for Site Response and Soil Structure Interaction Analyses,'' (Agencywide Documents... Soil Structure Interaction Analyses,'' (ADAMS Accession No. ML092230455) to solicit public and industry...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

This report was prepared at the request of the Lawrence Livermore Laboratory (LLL) to provide background information for analyzing soil-structure interaction by the frequency-independent impedance function approach. LLL is conducting such analyses as part of its seismic review of selected operating plants under the Systematic Evaluation Program for the US Nuclear Regulatory Commission. The analytical background and basic assumptionsof the impedance function theory are briefly reviewed, and the role of radiation damping in soil-structure interaction analysis is discussed. The validity of modeling soil-structure interaction by using frequency-independent functions is evaluated based on data from several field tests. Finally, the recommendedmore » procedures for performing soil-structure interaction analyses are discussed with emphasis on the modal superposition method.« less

Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri.

PubMed

Stein, Ricardo J; Höreth, Stephan; de Melo, J Romário F; Syllwasschy, Lara; Lee, Gwonjin; Garbin, Mário L; Clemens, Stephan; Krämer, Ute

2017-02-01

Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and successional trajectories in plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study we sought to examine how emblematic shifts from early-successional Alnus sinuata (alder) to late successional Picea sitchensis (spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield tomore » delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early-successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate drives shifts in the relative abundance of major taxa of bacteria in alder-influenced soils, including declines in those that are enriched by alder. We found these effects to be spruce-specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Our results show that spruce leachate addition more strongly structures bacterial communities than alders (less dispersion in bacterial community beta diversity). Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.« less

78 FR 13097 - Electric Power Research Institute; Seismic Evaluation Guidance

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-26

... outcrop motion for which the soil layers above the foundation elevation have been removed. Updating the... performing soil-structure interaction analyses. Consistent with guidance described in DC/COL-ISG-017, ``Ensuring Hazard-Consistent Seismic Input for Site Response and Soil Structure Interaction Analyses,'' the...

Combining Sequential Extractions and X-ray Absorption Spectroscopy for Quantitative and Qualitative Zinc Speciation in Soil

NASA Astrophysics Data System (ADS)

Bauer, Tatiana; Minkina, Tatiana; Batukaev, Abdulmalik; Nevidomskaya, Dina; Burachevskaya, Marina; Tsitsuashvili, Viktoriya; Urazgildieva, Kamilya

2017-04-01

The combined use of X-ray absorption spectrometry and extractive fractionation is an effective approach for studying the interaction of metal ions with soil compounds and identifying the phases-carriers of metals in soil and their stable fixation. These studies were carried out using the technique of X-ray absorption spectroscopy and chemical extractive fractionation. In a model experiment the samples taken in Calcic Chernozem were artificially contaminated with higher portion of Zn(NO3)2 (2000 mg/kg). The metal were incubated in soil samples for 2 year. The samples of soil mineral and organic phases (calcite, kaolinite, bentonite, humic acids) were saturated with Zn2+ from a solution of nitrate salts of metal. The total content of Zn in soil and soil various phases was determined using the X-ray fluorescence method. Extended X-ray absorption fine structure (EXAFS) Zn was measured at the Structural Materials Science beamline of the Kurchatov Center for Synchrotron Radiation. Sequential fractionation of Zn in soil conducted by Tessier method (Tessier et al., 1979) which determining 5 fractions of metals in soil: exchangeable, bound to Fe-Mn oxide, bound to carbonate, bound to the organic matter, and bound to silicate (residual). This methodology has so far more than 4000 citations (Web of Science), which demonstrates the popularity of this approach. Much Zn compounds are contained in uncontaminated soils in stable primary and secondary silicates inherited from the parental rocks (67% of the total concentrations in all fractions), which is a regional trait of soils in the fore-Caucasian plain. Extracted fractionation of metal compounds in soil samples, artificially contaminated with Zn salts, indicates the priority holding of Zn2+ ions by silicates, carbonates and Fe-Mn oxides. The Zn content significantly increases in the exchangeable fraction. Atomic structure study of the soil various phases saturated with Zn2+ ion by using (XANES) X-ray absorption spectroscopy allowed the determination of mechanism of metal ions interaction with soil phases and the resulting types of chemical bonds. Interaction with soil components modifies the electron structure of the metal ions themselves. The soil contamination with Zn is accompanied by decreasing the stable connection between metal and soil components. Interacting with humic acids in chernozem, the Zn2+ ion is coordinated by functional groups and ligands and forms unstable outer-sphere complexes. Zinc included into octahedral structures of layered minerals and hydro(oxides) can be inner-and outer-sphere adsorbed. The Zn2+ ions enable to replace Ca2+ ions in octahedral positions being coordinated with carbonate ions as ligands, thus forming absorbed complexes at the surface of mineral calcite. This work was supported by grant of the Russian Scientific Foundation № 16-14-10217.

Crossing Phenomena in Overhead Line Equipment (OHLE) Structure in 3D Space Considering Soil-Structure Interaction

NASA Astrophysics Data System (ADS)

Ngamkhanong, Chayut; Kaewunruen, Sakdirat; Baniotopoulos, Charalampos; Papaelias, Mayorkinos

2017-10-01

Nowadays, the electric train becomes one of the efficient railway systems that are lighter, cleaner, quieter, cheaper and faster than a conventional train. Overhead line equipment (OHLE), which supplies electric power to the trains, is designed on the principle of overhead wires placed over the railway track. The OHLE is supported by mast structure which located at the lineside along the track. Normally, mast structure is a steel column or truss structure which supports the overhead wire carrying the power. Due to the running train and severe periodic force, such as an earthquake, in surrounding area may cause damage to the OHLE structure especially mast structure which leads to the failure of the electrical system. The mast structure needs to be discussed in order to resist the random forces. Due to the vibration effect, the natural frequencies of the structure are necessary. This is because when the external applied force occurs within a range of frequency of the structure, resonance effect can be expected which lead to the large oscillations and deflections. The natural frequency of a system is dependent only on the stiffness of the structure and the mass which participates with the structure, including self-weight. The modal analysis is used in order to calculate the mode shapes and natural frequencies of the mast structure during free vibration. A mast structure with varying rotational soil stiffness is used to observe the influence of soil-structure action. It is common to use finite element analysis to perform a modal analysis. This paper presents the fundamental mode shapes, natural frequencies and crossing phenomena of three-dimensional mast structure considering soil-structure interaction. The sensitivity of mode shapes to the variation of soil-structure interaction is discussed. The outcome of this study will improve the understanding of the fundamental dynamic behaviour of the mast structure which supports the OHLE. Moreover, this study will be a recommendation for the structural engineer to associate with the behaviour of mast structure during vibration.

Development and assessment of transparent soil and particle image velocimetry in dynamic soil-structure interaction

DOT National Transportation Integrated Search

2007-02-01

This research combines Particle Image Velocimetry (PIV) and transparent soil to investigate the dynamic rigid block and soil interaction. In order to get a low viscosity pore fluid for the transparent soil, 12 different types of chemical solvents wer...

Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic.

PubMed

Xiao, Enzong; Krumins, Valdis; Xiao, Tangfu; Dong, Yiran; Tang, Song; Ning, Zengping; Huang, Zhengyu; Sun, Weimin

2017-02-01

Investigation of microbial communities of soils contaminated by antimony (Sb) and arsenic (As) is necessary to obtain knowledge for their bioremediation. However, little is known about the depth profiles of microbial community composition and structure in Sb and As contaminated soils. Our previous studies have suggested that historical factors (i.e., soil and sediment) play important roles in governing microbial community structure and composition. Here, we selected two different types of soil (flooded paddy soil versus dry corn field soil) with co-contamination of Sb and As to study interactions between these metalloids, geochemical parameters and the soil microbiota as well as microbial metabolism in response to Sb and As contamination. Comprehensive geochemical analyses and 16S rRNA amplicon sequencing were used to shed light on the interactions of the microbial communities with their environments. A wide diversity of taxonomical groups was present in both soil cores, and many were significantly correlated with geochemical parameters. Canonical correspondence analysis (CCA) and co-occurrence networks further elucidated the impact of geochemical parameters (including Sb and As contamination fractions and sulfate, TOC, Eh, and pH) on vertical distribution of soil microbial communities. Metagenomes predicted from the 16S data using PICRUSt included arsenic metabolism genes such as arsenate reductase (ArsC), arsenite oxidase small subunit (AoxA and AoxB), and arsenite transporter (ArsA and ACR3). In addition, predicted abundances of arsenate reductase (ArsC) and arsenite oxidase (AoxA and AoxB) genes were significantly correlated with Sb contamination fractions, These results suggest potential As biogeochemical cycling in both soil cores and potentially dynamic Sb biogeochemical cycling as well. Copyright © 2016 Elsevier Ltd. All rights reserved.

Unravelling Linkages between Plant Community Composition and the Pathogen-Suppressive Potential of Soils

PubMed Central

Latz, Ellen; Eisenhauer, Nico; Rall, Björn Christian; Scheu, Stefan; Jousset, Alexandre

2016-01-01

Plant diseases cause dramatic yield losses worldwide. Current disease control practices can be deleterious for the environment and human health, calling for alternative and sustainable management regimes. Soils harbour microorganisms that can efficiently suppress pathogens. Uncovering mediators driving their functioning in the field still remains challenging, but represents an essential step in order to develop strategies for increased soil health. We set up plant communities of varying richness to experimentally test the potential of soils differing in plant community history to suppress the pathogen Rhizoctonia solani. The results indicate that plant communities shape soil-disease suppression via changes in abiotic soil properties and the abundance of bacterial groups including species of the genera Actinomyces, Bacillus and Pseudomonas. Further, the results suggest that pairwise interactions between specific plant species strongly affect soil suppressiveness. Using structural equation modelling, we provide a pathway orientated framework showing how the complex interactions between plants, soil and microorganisms jointly shape soil suppressiveness. Our results stress the importance of plant community composition as a determinant of soil functioning, such as the disease suppressive potential of soils. PMID:27021053

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession.

PubMed

Knelman, Joseph E; Graham, Emily B; Prevéy, Janet S; Robeson, Michael S; Kelly, Patrick; Hood, Eran; Schmidt, Steve K

2018-01-01

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession

PubMed Central

Knelman, Joseph E.; Graham, Emily B.; Prevéy, Janet S.; Robeson, Michael S.; Kelly, Patrick; Hood, Eran; Schmidt, Steve K.

2018-01-01

Past research demonstrating the importance plant–microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant–microbe interactions with late-successional plants and interspecific plant interactions more generally. PMID:29467741

Reliability-based design optimization of reinforced concrete structures including soil-structure interaction using a discrete gravitational search algorithm and a proposed metamodel

NASA Astrophysics Data System (ADS)

Khatibinia, M.; Salajegheh, E.; Salajegheh, J.; Fadaee, M. J.

2013-10-01

A new discrete gravitational search algorithm (DGSA) and a metamodelling framework are introduced for reliability-based design optimization (RBDO) of reinforced concrete structures. The RBDO of structures with soil-structure interaction (SSI) effects is investigated in accordance with performance-based design. The proposed DGSA is based on the standard gravitational search algorithm (GSA) to optimize the structural cost under deterministic and probabilistic constraints. The Monte-Carlo simulation (MCS) method is considered as the most reliable method for estimating the probabilities of reliability. In order to reduce the computational time of MCS, the proposed metamodelling framework is employed to predict the responses of the SSI system in the RBDO procedure. The metamodel consists of a weighted least squares support vector machine (WLS-SVM) and a wavelet kernel function, which is called WWLS-SVM. Numerical results demonstrate the efficiency and computational advantages of DGSA and the proposed metamodel for RBDO of reinforced concrete structures.

How soil organic matter composition controls hexachlorobenzene-soil-interactions: adsorption isotherms and quantum chemical modeling.

PubMed

Ahmed, Ashour A; Kühn, Oliver; Aziz, Saadullah G; Hilal, Rifaat H; Leinweber, Peter

2014-04-01

Hazardous persistent organic pollutants (POPs) interact in soil with the soil organic matter (SOM) but this interaction is insufficiently understood at the molecular level. We investigated the adsorption of hexachlorobenzene (HCB) on soil samples with systematically modified SOM. These samples included the original soil, the soil modified by adding a hot water extract (HWE) fraction (soil+3 HWE and soil+6 HWE), and the pyrolyzed soil. The SOM contents increased in the order pyrolyzed soil

Response of soil biota to vineyard interrow soil cultivation can be altered by the surrounding landscape

NASA Astrophysics Data System (ADS)

Zaller, Johann; Buchholz, Jacob; Querner, Pascal; Paredes, Daniel; Kratschmer, Sophie; Schwantzer, Martina; Winter, Silvia; Strauss, Peter; Bauer, Thomas; Burel, Françoise; Guernion, Muriel; Scimia, Jennifer; Nicolai, Annegret; Cluzeau, Daniel

2017-04-01

Ecosystem services provided by viticultural landscapes result from interactions between management intensity, soil properties, organisms inhabiting these landscapes, and the diversity and structure of the surrounding landscape. However, there is actually very little known to what extent these different factors influence the abundance and diversity of various soil biota. In this study we examined (i) to what extent different soil management intensities of interrows affect the activity and diversity of soil biota (earthworms, Collembola, litter decomposition), (ii) the role of soil properties in influencing these effects and (iii) whether the surrounding landscape structure is altering these interactions. We collected data in 16 vineyards in Austria embedded in landscapes with varying structure (i.e. from structurally simple to complex) and assessed earthworms (hand sorting), Collembola (pitfall trapping and soil coring), litter decomposition (tea bag method). Additionally, soil physical (water infiltration, aggregate stability, porosity, bulk density, soil texture) and chemical (pH, soil carbon content, cation exchange capacity, potassium, phosphorus) parameters were assessed. The landscape surrounding our vineyards within a radius of 750 m was assessed by field mapping using a geographical information system. Results showed that different soil biota/processes are differently affected by soil cultivation intensity and soil properties. Parameters describing the surrounding landscape interacted more with the responses of Collembola to soil cultivation than with earthworms or litter decomposition. These investigations are part of the transdisciplinary BiodivERsA project VineDivers (www.vinedivers.eu) and will ultimately lead into management recommendations for various stakeholders.

Soil-structure interaction studies for understanding the behavior of integral abutment bridges.

DOT National Transportation Integrated Search

2012-03-01

Integral Abutment Bridges (IAB) are bridges without any joints within the bridge deck or between the : superstructure and the abutments. An IAB provides many advantages during construction and maintenance of : a bridge. Soil-structure interactions at...

Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing

PubMed Central

Penton, C. Ryan; Gupta, V. V. S. R.; Tiedje, James M.; Neate, Stephen M.; Ophel-Keller, Kathy; Gillings, Michael; Harvey, Paul; Pham, Amanda; Roget, David K.

2014-01-01

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils ‘suppressive’ or ‘non-suppressive’ for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. PMID:24699870

Combined wave propagation analysis of earthquake recordings from borehole and building sensors

NASA Astrophysics Data System (ADS)

Petrovic, B.; Parolai, S.; Dikmen, U.; Safak, E.; Moldobekov, B.; Orunbaev, S.

2015-12-01

In regions highly exposed to natural hazards, Early Warning Systems can play a central role in risk management and mitigation procedures. To improve at a relatively low cost the spatial resolution of regional earthquake early warning (EEW) systems, decentralized onsite EEW and building monitoring, a wireless sensing unit, the Self-Organizing Seismic Early Warning Information Network (SOSEWIN) was developed and further improved to include the multi-parameter acquisition. SOSEWINs working in continuous real time mode are currently tested on various sites. In Bishkek and Istanbul, an instrumented building is located close to a borehole equipped with downhole sensors. The joint data analysis of building and borehole earthquake recordings allows the study of the behavior of the building, characteristics of the soil, and soil-structure interactions. The interferometric approach applied to recordings of the building response is particularly suitable to characterize the wave propagation inside a building, including the propagation velocity of shear waves and attenuation. Applied to borehole sensors, it gives insights into velocity changes in different layers, reflections and mode conversion, and allows the estimation of the quality factor Qs. We used combined building and borehole data from the two test sites: 1) to estimate the characteristics of wave propagation through the building to the soil and back, and 2) to obtain an empirical insight into soil-structure interactions. The two test sites represent two different building and soil types, and soil structure impedance contrasts. The wave propagation through the soil to the building and back is investigated by the joint interferometric approach. The propagation of up and down-going waves through the building and soil is clearly imaged and the reflection of P and S waves from the earth surface and the top of the building identified. An estimate of the reflected and transmitted energy amounts is given, too.

A soil-landscape framework for understanding spatial and temporal variability in biogeochemical processes in catchments

NASA Astrophysics Data System (ADS)

McGuire, K. J.; Bailey, S. W.; Ross, D. S.

2017-12-01

Heterogeneity in biophysical properties within catchments challenges how we quantify and characterize biogeochemical processes and interpret catchment outputs. Interactions between the spatiotemporal variability of hydrological states and fluxes and soil development can spatially structure catchments, leading to a framework for understanding patterns in biogeochemical processes. In an upland, glaciated landscape at the Hubbard Brook Experimental Forest (HBEF) in New Hampshire, USA, we are embracing the structure and organization of soils to understand the spatial relations between runoff production zones, distinct soil-biogeochemical environments, and solute retention and release. This presentation will use observations from the HBEF to demonstrate that a soil-landscape framework is essential in understanding the spatial and temporal variability of biogeochemical processes in this catchment. Specific examples will include how laterally developed soils reveal the location of active runoff production zones and lead to gradients in primary mineral dissolution and the distribution of weathering products along hillslopes. Soil development patterns also highlight potential carbon and nitrogen cycling hotspots, differentiate acidic conditions, and affect the regulation of surface water quality. Overall, this work demonstrates the importance of understanding the landscape-level structural organization of soils in characterizing the variation and extent of biogeochemical processes that occur in catchments.

Possibilities of the particle finite element method for fluid-soil-structure interaction problems

NASA Astrophysics Data System (ADS)

Oñate, Eugenio; Celigueta, Miguel Angel; Idelsohn, Sergio R.; Salazar, Fernando; Suárez, Benjamín

2011-09-01

We present some developments in the particle finite element method (PFEM) for analysis of complex coupled problems in mechanics involving fluid-soil-structure interaction (FSSI). The PFEM uses an updated Lagrangian description to model the motion of nodes (particles) in both the fluid and the solid domains (the later including soil/rock and structures). A mesh connects the particles (nodes) defining the discretized domain where the governing equations for each of the constituent materials are solved as in the standard FEM. The stabilization for dealing with an incompressibility continuum is introduced via the finite calculus method. An incremental iterative scheme for the solution of the non linear transient coupled FSSI problem is described. The procedure to model frictional contact conditions and material erosion at fluid-solid and solid-solid interfaces is described. We present several examples of application of the PFEM to solve FSSI problems such as the motion of rocks by water streams, the erosion of a river bed adjacent to a bridge foundation, the stability of breakwaters and constructions sea waves and the study of landslides.

Soil fungi colony growth and community dynamics

NASA Astrophysics Data System (ADS)

Falconer, Ruth E.; Kravchenko, Alexandra; Otten, Wilfred

2010-05-01

Fungi are a major player in soil functioning, they contribute to soil structure formation and shaping of plant communities through their role in nutrient cycling, pathogenesis and symbiosis. Theoretical approaches which have emerged over the years and improved considerably our understanding of above ground plant communities are still lacking below ground. A theoretical framework is needed, such that links soil physics, fungal biology and mathematical biology in order to understand fungal community dynamics and diversity in undisturbed soils. Such a framework is essential if we are to understand how environmental change or soil manipulation impacts biodiversity. Different land use and management practices significantly affect soil environmental characteristics crucial for fungal communities by contributing different quantities and qualities of biomass inputs, generating different levels of soil disturbance, influencing soil temperature and moisture regimes, and affecting structure and geometry of soil pore space. Differences in pore structures generated by long-term differences in land use and management are reflected in notable changes in soil physical and hydraulic properties, including soil porosity, hydraulic conductivity and water retention (Brye and Pirani, 2005). Changes in numbers, shapes, and distributions of soil macropores have been often observed (e.g., Pachepsky et al., 1996; Giménez et al., 1997; Udawatta et al., 2008). However, specific implications of these differences in pore structure and geometries for ability of pathogenic as well as non-pathogenic fungi to colonize soil have not yet been addressed. Recent advances in computed tomography and microscopy facilitate detailed examination of the inner pore structures of undisturbed soil samples as well as visualization of fungal mycelia. Such tools together with modelling generate a new level of understanding of the mechanisms governing fungal behaviour at microscopic scales, and for the first time allow us to examine species interactions in a 3D soil environment.

75 FR 36715 - Advisory Committee on Reactor Safeguards; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

... Seismic Input for Site Response and Soil Structure Interaction Analyses'' (Open)--The Committee will hold... Seismic Input for Site Response and Soil Structure Interaction Analyses.'' 9:30 a.m.-10:30 a.m.: Interim Staff Guidance (ISG) DC/COL-ISG-020, ``Implementation of Seismic Margin Analysis for New Reactors Based...

Deciphering biodegradable chelant-enhanced phytoremediation through microbes and nitrogen transformation in contaminated soils.

PubMed

Fang, Linchuan; Wang, Mengke; Cai, Lin; Cang, Long

2017-06-01

Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.

In-situ molecular-level elucidation of organofluorine binding sites in a whole peat soil.

PubMed

Longstaffe, James G; Courtier-Murias, Denis; Soong, Ronald; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Hutchins, Howard; Krishnamurthy, Sridevi; Struppe, Jochem; Alaee, Mehran; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, André J

2012-10-02

The chemical nature of xenobiotic binding sites in soils is of vital importance to environmental biogeochemistry. Interactions between xenobiotics and the naturally occurring organic constituents of soils are strongly correlated to environmental persistence, bioaccessibility, and ecotoxicity. Nevertheless, because of the complex structural and chemical heterogeneity of soils, studies of these interactions are most commonly performed indirectly, using correlative methods, fractionation, or chemical modification. Here we identify the organic components of an unmodified peat soil where some organofluorine xenobiotic compounds interact using direct molecular-level methods. Using (19)F→(1)H cross-polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, the (19)F nuclei of organofluorine compounds are used to induce observable transverse magnetization in the (1)H nuclei of organic components of the soil with which they interact after sorption. The observed (19)F→(1)H CP-MAS spectra and dynamics are compared to those produced using model soil organic compounds, lignin and albumin. It is found that lignin-like components can account for the interactions observed in this soil for heptafluoronaphthol (HFNap) while protein structures can account for the interactions observed for perfluorooctanoic acid (PFOA). This study employs novel comprehensive multi-phase (CMP) NMR technology that permits the application of solution-, gel-, and solid-state NMR experiments on intact soil samples in their swollen state.

Microbial Ecology of Soil Aggregation in Agroecosystems

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences in the abundance of chemical classes in clay loams compared to sandy loams. Together our data demonstrate that the potential for aggregation and C storage is strongly influenced by soil mineralogy with important implications for plant-microbe interactions that mediate C biogeochemistry.

Out-of-plane (SH) soil-structure interaction: a shear wall with rigid and flexible ring foundation

NASA Astrophysics Data System (ADS)

Le, Thang; Lee, Vincent W.; Luo, Hao

2016-02-01

Soil-structure interaction (SSI) of a building and shear wall above a foundation in an elastic half-space has long been an important research subject for earthquake engineers and strong-motion seismologists. Numerous papers have been published since the early 1970s; however, very few of these papers have analytic closed-form solutions available. The soil-structure interaction problem is one of the most classic problems connecting the two disciplines of earthquake engineering and civil engineering. The interaction effect represents the mechanism of energy transfer and dissipation among the elements of the dynamic system, namely the soil subgrade, foundation, and superstructure. This interaction effect is important across many structure, foundation, and subgrade types but is most pronounced when a rigid superstructure is founded on a relatively soft lower foundation and subgrade. This effect may only be ignored when the subgrade is much harder than a flexible superstructure: for instance a flexible moment frame superstructure founded on a thin compacted soil layer on top of very stiff bedrock below. This paper will study the interaction effect of the subgrade and the superstructure. The analytical solution of the interaction of a shear wall, flexible-rigid foundation, and an elastic half-space is derived for incident SH waves with various angles of incidence. It found that the flexible ring (soft layer) cannot be used as an isolation mechanism to decouple a superstructure from its substructure resting on a shaking half-space.

Testing the Visual Soil Assessment tool on Estonian farm fields

NASA Astrophysics Data System (ADS)

Reintam, Endla; Are, Mihkel; Selge, Are

2017-04-01

Soil quality estimation plays important role in decision making on farm as well on policy level. Sustaining the production ability and good health of the soil the chemical, physical and biological indicators should be taken into account. The system to use soil chemical parameters is usually quite well established in most European counties, including Estonia. However, measuring soil physical properties, such bulk density, porosity, penetration resistance, structural stability ect is time consuming, needs special tools and is highly weather dependent. In that reason these parameters are excluded from controllable quality parameters in policy in Estonia. Within the project "Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience" (iSQAPER) the visual soil assessment (VSA) tool was developed for easy detection of soil quality as well the different soil friendly agricultural management practices (AMP) were detected. The aim of current study was to test the VSA tool on Estonian farm fields under different management practices and compare the results with laboratory measurements. The main focus was set on soil physical parameters. Next to the VSA, the undisturbed soil samples were collected from the depth of 5-10 cm and 25-30 cm. The study revealed that results of a visually assessed soil physical parameters, such a soil structure, soil structural stability, soil porosity, presence of tillage pan, were confirmed by laboratory measurements in most cases. Soil water stable structure measurement on field (on 1 cm2 net in one 1 l box with 4-6 cm air dry clods for 5-10 min) underestimated very well structured soil on grassland and overestimated the structure aggregates stability of compacted soil. The slightly better soil quality was detected under no-tillage compared to ploughed soils. However, the ploughed soil got higher quality points compared with minimum tillage. The slurry application (organic manuring) had controversial impact - it increased the number of earthworms but decreased soil structural stability. Even the manuring with slurry increases organic matter amount in the soil, the compaction due to the use of heavy machinery during the application, especially on wet soil, reduces the positive effect of slurry.

Optimization of the time series NDVI-rainfall relationship using linear mixed-effects modeling for the anti-desertification area in the Beijing and Tianjin sandstorm source region

NASA Astrophysics Data System (ADS)

Wang, Jin; Sun, Tao; Fu, Anmin; Xu, Hao; Wang, Xinjie

2018-05-01

Degradation in drylands is a critically important global issue that threatens ecosystem and environmental in many ways. Researchers have tried to use remote sensing data and meteorological data to perform residual trend analysis and identify human-induced vegetation changes. However, complex interactions between vegetation and climate, soil units and topography have not yet been considered. Data used in the study included annual accumulated Moderate Resolution Imaging Spectroradiometer (MODIS) 250 m normalized difference vegetation index (NDVI) from 2002 to 2013, accumulated rainfall from September to August, digital elevation model (DEM) and soil units. This paper presents linear mixed-effect (LME) modeling methods for the NDVI-rainfall relationship. We developed linear mixed-effects models that considered the random effects of sample points nested in soil units for nested two-level modeling and single-level modeling of soil units and sample points, respectively. Additionally, three functions, including the exponential function (exp), the power function (power), and the constant plus power function (CPP), were tested to remove heterogeneity, and an additional three correlation structures, including the first-order autoregressive structure [AR(1)], a combination of first-order autoregressive and moving average structures [ARMA(1,1)] and the compound symmetry structure (CS), were used to address the spatiotemporal correlations. It was concluded that the nested two-level model considering both heteroscedasticity with (CPP) and spatiotemporal correlation with [ARMA(1,1)] showed the best performance (AMR = 0.1881, RMSE = 0.2576, adj- R 2 = 0.9593). Variations between soil units and sample points that may have an effect on the NDVI-rainfall relationship should be included in model structures, and linear mixed-effects modeling achieves this in an effective and accurate way.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coleman, Justin; Slaughter, Andrew; Veeraraghavan, Swetha

Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON) is a finite element application that aims at analyzing the response of 3-D soil-structure systems to natural and man-made hazards such as earthquakes, floods and fire. MASTODON currently focuses on the simulation of seismic events and has the capability to perform extensive ‘source-to-site’ simulations including earthquake fault rupture, nonlinear wave propagation and nonlinear soil-structure interaction (NLSSI) analysis. MASTODON is being developed to be a dynamic probabilistic risk assessment framework that enables analysts to not only perform deterministic analyses, but also easily perform probabilistic or stochastic simulations for the purpose of risk assessment.

Study on soil-pile-structure-TMD interaction system by shaking table model test

NASA Astrophysics Data System (ADS)

Lou, Menglin; Wang, Wenjian

2004-06-01

The success of the tuned mass damper (TMD) in reducing wind-induced structural vibrations has been well established. However, from most of the recent numerical studies, it appears that for a structure situated on very soft soil, soil-structure interaction (SSI) could render a damper on the structure totally ineffective. In order to experimentally verify the SSI effect on the seismic performance of TMD, a series of shaking table model tests have been conducted and the results are presented in this paper. It has been shown that the TMD is not as effective in controlling the seismic responses of structures built on soft soil sites due to the SSI effect. Some test results also show that a TMD device might have a negative impact if the SSI effect is neglected and the structure is built on a soft soil site. For structures constructed on a soil foundation, this research verifies that the SSI effect must be carefully understood before a TMD control system is designed to determine if the control is necessary and if the SSI effect must be considered when choosing the optimal parameters of the TMD device.

Effect of Soil Washing for Lead and Zinc Removal on Soil Hydraulic Properties

NASA Astrophysics Data System (ADS)

Kammerer, Gerhard; Zupanc, Vesna; Gluhar, Simon; Lestan, Domen

2017-04-01

Soil washing as a metal pollution remediation process, especially part with intensive mixing of the soil slurry and soil compression after de-watering, significantly deteriorates physical properties of soil compared to those of non-remediated soil. Furthermore, changed physical characteristics of remediated soil influence interaction of plant roots with soil system and affect soil water regime. Remediated soils showed significant differences to their original state in water retention properties and changed structure due to the influence of artificial structure created during remediation process. Disturbed and undisturbed soil samples of remediated and original soils were analyzed. We evaluated soil hydraulic properties as a possible constraint for re-establishing soil structure and soil fertility after the remediation procedure.

Investigation of deformation of elements of three-dimensional reinforced concrete structures located in the soil, interacting with each other through rubber gaskets

NASA Astrophysics Data System (ADS)

Berezhnoi, D. V.; Balafendieva, I. S.; Sachenkov, A. A.; Sekaeva, L. R.

2017-06-01

In work the technique of calculation of elements of three-dimensional reinforced concrete substructures located in a soil, interacting with each other through rubber linings is realized. To describe the interaction of deformable structures with the ground, special “semi-infinite” finite elements are used. A technique has been implemented that allows one to describe the contact interaction of three-dimensional structures by means of a special contact finite element with specific properties. The obtained numerical results are compared with the experimental data, their good agreement is noted.

Soils and public health: the vital nexus

NASA Astrophysics Data System (ADS)

Pachepsky, Yakov

2015-04-01

Soils sustain life. They affect human health via quantity, quality, and safety of available food and water, and via direct exposure of individuals to soils. Throughout the history of civilization, soil-health relationships have inspired spiritual movements, philosophical systems, cultural exchanges, and interdisciplinary interactions, and provided medicinal substances of paramount impact. Given the climate, resource, and population pressures, understanding and managing the soil-health interactions becomes a modern imperative. We are witnessing a paradigm shift from recognizing and yet disregarding the 'soil-health' nexus complexity to parameterizing this complexity and identifying reliable controls. This becomes possible with the advent of modern research tools as a source of 'big data' on multivariate nonlinear soil systems and the multiplicity of health metrics. The phenomenon of suppression of human pathogens in soils and plants presents a recent example of these developments. Evidence is growing about the dependence of pathogen suppression on the soil microbial community structure which, in turn, is affected by the soil-plant system management. Soil eutrophication appears to create favorable conditions for pathogen survival. Another example of promising information-rich research considers links and feedbacks between the soil microbial community structure and structure of soil physical pore space. The two structures are intertwined and involved in the intricate self-organization that controls soil services to public health. This, in particular, affects functioning of soils as a powerful water filter and the capacity of this filter with respect to emerging contaminants in both 'green' and 'blue' waters. To evaluate effects of soil services to public health, upscaling procedures are needed for relating the fine-scale mechanistic knowledge to available coarse-scale information on soil properties and management. More needs to be learned about health effects of soils in organic agriculture that are often used for soil quality comparison and benchmarking. The influence of soil degradation and rehabilitation on public health has to be assessed in quantitative terms. Some links between soils and public health regarding, for example, immune maturation, antibiotic resistance development, and mental well-being, have been long hypothesized but remain to be examined. The data on soil-health relationships are scarce and very much disjointed, and a concerted international effort appears to be needed to encompass various economic and geographical settings. Current definitions of healthy soil broadly include aspects that are conducive for human health, and functional evaluation of soil quality with a focus on public health will have useful applications in public policies and perception. The 'soil-health' connection is complex in character, global in manifestation, and applicable to every human being.

Visualization of the tire-soil interaction area by means of ObjectARX programming interface

NASA Astrophysics Data System (ADS)

Mueller, W.; Gruszczyński, M.; Raba, B.; Lewicki, A.; Przybył, K.; Zaborowicz, M.; Koszela, K.; Boniecki, P.

2014-04-01

The process of data visualization, important for their analysis, becomes problematic when large data sets generated via computer simulations are available. This problem concerns, among others, the models that describe the geometry of tire-soil interaction. For the purpose of a graphical representation of this area and implementation of various geometric calculations the authors have developed a plug-in application for AutoCAD, based on the latest technologies, including ObjectARX, LINQ and the use of Visual Studio platform. Selected programming tools offer a wide variety of IT structures that enable data visualization and data analysis and are important e.g. in model verification.

Calibrating Nonlinear Soil Material Properties for Seismic Analysis Using Soil Material Properties Intended for Linear Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spears, Robert Edward; Coleman, Justin Leigh

2015-08-01

Seismic analysis of nuclear structures is routinely performed using guidance provided in “Seismic Analysis of Safety-Related Nuclear Structures and Commentary (ASCE 4, 1998).” This document, which is currently under revision, provides detailed guidance on linear seismic soil-structure-interaction (SSI) analysis of nuclear structures. To accommodate the linear analysis, soil material properties are typically developed as shear modulus and damping ratio versus cyclic shear strain amplitude. A new Appendix in ASCE 4-2014 (draft) is being added to provide guidance for nonlinear time domain SSI analysis. To accommodate the nonlinear analysis, a more appropriate form of the soil material properties includes shear stressmore » and energy absorbed per cycle versus shear strain. Ideally, nonlinear soil model material properties would be established with soil testing appropriate for the nonlinear constitutive model being used. However, much of the soil testing done for SSI analysis is performed for use with linear analysis techniques. Consequently, a method is described in this paper that uses soil test data intended for linear analysis to develop nonlinear soil material properties. To produce nonlinear material properties that are equivalent to the linear material properties, the linear and nonlinear model hysteresis loops are considered. For equivalent material properties, the shear stress at peak shear strain and energy absorbed per cycle should match when comparing the linear and nonlinear model hysteresis loops. Consequently, nonlinear material properties are selected based on these criteria.« less

Pesticide interactions with soil affected by olive mill wastewater (OMW): how strong and long-lasting is the OMW effect?

NASA Astrophysics Data System (ADS)

Keren, Yonatan; Borisover, Mikhail; Schaumann, Gabriele E.; Diehl, Dörte; Tamimi, Nisreen; Bukhanovsky, Nadezhda

2017-04-01

Sorption interactions with soils are well known to control the environmental fate of multiple organic compounds including pesticides. Pesticide-soil interactions may be affected by organic amendments or organic matter (OM)-containing wastewater brought to the field. Specifically, land spreading of olive mill wastewater (OMW), occurring intentionally or not, may also influence pesticide-soil interactions. The effects of the OMW disposed in the field on soil properties, including their ability to interact with pesticides, become of great interest due to the increasing demand for olive oil and a constant growth of world oil production. This paper summarizes some recent findings related to the effect of prior OMW land application on the ability of soils to interact with the organic compounds including pesticides, diuron and simazine. The major findings are as following: (1) bringing OMW to the field increases the potential of soils to sorb non-ionized pesticides; (2) this sorption increase may not be related solely to the increase in soil organic carbon content but it can reflect also the changes in the soil sorption mechanisms; (3) increased pesticide interactions with OMW-affected soils may become irreversible, due, assumedly, to the swelling of some components of the OMW-treated soil; (4) enhanced pesticide-soil interactions mitigate with the time passed after the OMW application, however, in the case of diuron, the remaining effect could be envisioned at least 600 days after the normal OMW application; (5) the enhancement effect of OMW application on soil sorption may increase with soil depth, in the 0-10 cm interval; (6) at higher pesticide (diuron) concentrations, larger extents of sorption enhancement, following the prior OMW-soil interactions, may be expected; (7) disposal of OMW in the field may be seasonal-dependent, and, in the case studied, it led to more distinct impacts on sorption when carried out in spring and winter, as compared with summer. It appears that when examining the fate of organic compounds in soil environments affected by OMW, more attention is needed to (a) the effect of the OMW penetration into the depth on soil-pesticide interactions; (b) long-term and seasonal-dependent effects of OMW application.

Methods to test the interactive effects of drought and plant invasion on ecosystem structure and function using complementary common garden and field experiments.

PubMed

Alba, Christina; NeSmith, Julienne E; Fahey, Catherine; Angelini, Christine; Flory, Stephen Luke

2017-03-01

Abiotic global change drivers affect ecosystem structure and function, but how they interact with biotic factors such as invasive plants is understudied. Such interactions may be additive, synergistic, or offsetting, and difficult to predict. We present methods to test the individual and interactive effects of drought and plant invasion on native ecosystems. We coupled a factorial common garden experiment containing resident communities exposed to drought (imposed with rainout shelters) and invasion with a field experiment where the invader was removed from sites spanning a natural soil moisture gradient. We detail treatments and their effects on abiotic conditions, including soil moisture, light, temperature, and humidity, which shape community and ecosystem responses. Ambient precipitation during the garden experiment exceeded historic norms despite severe drought in prior years. Soil moisture was 48% lower in drought than ambient plots, but the invader largely offset drought effects. Additionally, temperature and light were lower and humidity higher in invaded plots. Field sites spanned up to a 10-fold range in soil moisture and up to a 2.5-fold range in light availability. Invaded and resident vegetation did not differentially mediate soil moisture, unlike in the garden experiment. Herbicide effectively removed invaded and resident vegetation, with removal having site-specific effects on soil moisture and light availability. However, light was generally higher in invader-removal than control plots, whereas resident removal had less effect on light, similar to the garden experiment. Invasion mitigated a constellation of abiotic conditions associated with drought stress in the garden experiment. In the field, where other factors co-varied, these patterns did not emerge. Still, neither experiment suggested that drought and invasion will have synergistic negative effects on ecosystems, although invasion can limit light availability. Coupling factorial garden experiments with field experiments across environmental gradients will be effective for predicting how multiple stressors interact in natural systems.

SEISMIC RESPONSE OF DAM WITH SOIL-STRUCTURE INTERACTION.

USGS Publications Warehouse

Bycroft, G.N.; Mork, P.N.

1987-01-01

An analytical solution to the response of a long trapezoidal-section dam on a foundation consisting of an elastic half-space and subjected to simulated earthquake motion is developed. An optimum seismic design is achieved when the cross section of the dam is triangular. The effect of soil structure interaction is to lower the strain occurring in the dam.

Determination of Martian soil mineralogy and water content using the Thermal Analyzer for Planetary Soils (TAPS)

NASA Technical Reports Server (NTRS)

Gooding, James L.; Ming, Douglas W.; Allton, Judith H.; Byers, Terry B.; Dunn, Robert P.; Gibbons, Frank L.; Pate, Daniel B.; Polette, Thomas M.

1992-01-01

Physical and chemical interactions between the surface and atmosphere of Mars can be expected to embody a strong cause-and-effect relationship with the minerals comprising the martian regolith. Many of the minerals in soils and sediments are probably products of chemical weathering (involving surface/atmosphere or surface/hydrosphere reactions) that could be expected to subsequently influence the sorption of atmospheric gases and water vapor. Therefore, identification of the minerals in martian surface soils and sediments is essential for understanding both past and present interactions between the Mars surface and atmosphere. Clearly, the most definitive mineral analyses would be achieved with well-preserved samples returned to Earth-based laboratories. In advance of a Mars sample return mission, however, significant progress could be made with in situ experiments that fill current voids in knowledge about the presence or abundance of key soil minerals such as clays (layered-structured silicates), zeolites, and various salts, including carbonates. TAPS is intended to answer that challenge by providing first-order identification of soil and sediment minerals.

Climate change driven plant-metal-microbe interactions.

PubMed

Rajkumar, Mani; Prasad, Majeti Narasimha Vara; Swaminathan, Sandhya; Freitas, Helena

2013-03-01

Various biotic and abiotic stress factors affect the growth and productivity of crop plants. Particularly, the climatic and/or heavy metal stress influence various processes including growth, physiology, biochemistry, and yield of crops. Climatic changes particularly the elevated atmospheric CO₂ enhance the biomass production and metal accumulation in plants and help plants to support greater microbial populations and/or protect the microorganisms against the impacts of heavy metals. Besides, the indirect effects of climatic change (e.g., changes in the function and structure of plant roots and diversity and activity of rhizosphere microbes) would lead to altered metal bioavailability in soils and concomitantly affect plant growth. However, the effects of warming, drought or combined climatic stress on plant growth and metal accumulation vary substantially across physico-chemico-biological properties of the environment (e.g., soil pH, heavy metal type and its bio-available concentrations, microbial diversity, and interactive effects of climatic factors) and plant used. Overall, direct and/or indirect effects of climate change on heavy metal mobility in soils may further hinder the ability of plants to adapt and make them more susceptible to stress. Here, we review and discuss how the climatic parameters including atmospheric CO₂, temperature and drought influence the plant-metal interaction in polluted soils. Other aspects including the effects of climate change and heavy metals on plant-microbe interaction, heavy metal phytoremediation and safety of food and feed are also discussed. This review shows that predicting how plant-metal interaction responds to altering climatic change is critical to select suitable crop plants that would be able to produce more yields and tolerate multi-stress conditions without accumulating toxic heavy metals for future food security. Copyright © 2012 Elsevier Ltd. All rights reserved.

Seismic analysis of the Mirror Fusion Test Facility: soil structure interaction analyses of the Axicell vacuum vessel. Revision 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maslenikov, O.R.; Mraz, M.J.; Johnson, J.J.

1986-03-01

This report documents the seismic analyses performed by SMA for the MFTF-B Axicell vacuum vessel. In the course of this study we performed response spectrum analyses, CLASSI fixed-base analyses, and SSI analyses that included interaction effects between the vessel and vault. The response spectrum analysis served to benchmark certain modeling differences between the LLNL and SMA versions of the vessel model. The fixed-base analysis benchmarked the differences between analysis techniques. The SSI analyses provided our best estimate of vessel response to the postulated seismic excitation for the MFTF-B facility, and included consideration of uncertainties in soil properties by calculating responsemore » for a range of soil shear moduli. Our results are presented in this report as tables of comparisons of specific member forces from our analyses and the analyses performed by LLNL. Also presented are tables of maximum accelerations and relative displacements and plots of response spectra at various selected locations.« less

Modeling soil processes - are we lost in diversity?

NASA Astrophysics Data System (ADS)

Vogel, Hans-Joerg; Schlüter, Steffen

2015-04-01

Soils are among the most complex environmental systems. Soil functions - e.g. production of biomass, habitat for organisms, reactor for and storage of organic matter, filter for ground water - emerge from a multitude of processes interacting at different scales. It still remains a challenge to model and predict these functions including their stability and resilience towards external perturbations. As an inherent property of complex systems it is prohibitive to unravel all the relevant process in all detail to derive soil functions and their dynamics from first principles. Hence, when modeling soil processes and their interactions one is close to be lost in the overwhelming diversity and spatial heterogeneity of soil properties. In this contribution we suggest to look for characteristic similarities within the hyperdimensional state space of soil properties. The underlying hypothesis is that this state space is not evenly and/or randomly populated but that processes of self organization produce attractors of physical, chemical and biological properties which can be identified. (The formation of characteristic soil horizons is an obvious example). To render such a concept operational a suitable and limited set of indicators is required. Ideally, such indicators are i) related to soil functions, ii) are measurable and iii) are integral measures of the relevant physical, chemical and biological soil properties. This would allow for identifying suitable attractors. We will discuss possible indicators and will focus on soil structure as an especially promising candidate. It governs the availability of water and gas, it effects the spatial distribution of organic matter and, moreover, it forms the habitat of soil organisms and it is formed by soil biota. Quantification of soil structural properties became possible only recently with the development of more powerful tools for non-invasive imaging. Future research need to demonstrate in how far these tools can be used to identify functional soil types (i.e. attractors) allowing for modeling soil processes at an integral level. We provide an example from the 100-years fertilization experiment in Bad-Lauchstädt.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

PubMed Central

2012-01-01

Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree. PMID:22873209

Effects of non-structural components and soil-structure interaction on the seismic response of framed structures

NASA Astrophysics Data System (ADS)

Ditommaso, Rocco; Auletta, Gianluca; Iacovino, Chiara; Nigro, Antonella; Carlo Ponzo, Felice

2017-04-01

In this paper, several nonlinear numerical models of reinforced concrete framed structures have been defined in order to evaluate the effects of non-structural elements and soil-structure interaction on the elastic dynamic behaviour of buildings. In the last few years, many and various studies have highlighted the significant effects derived from the interaction between structural and non-structural components on the main dynamic characteristics of a building. Usually, structural and non-structural elements act together, adding both masses and stiffness. The presence of infill panels is generally neglected in the design process of structural elements, although these elements can significantly increase the lateral stiffness of a structure leading to a modification in the dynamic properties. Particularly, at the Damage Limit State (where an elastic behaviour is expected), soil-structure interaction effects and non-structural elements may further affect the elastic natural period of buildings, changing the spectral accelerations compared with those provided by seismic codes in case of static analyses. In this work, a parametric study has been performed in order to evaluate the elastic fundamental period of vibration of buildings as a function of structural morphology (height, plan area, ratio between plan dimensions), infills presence and distribution and soil characteristics. Acknowledgements This study was partially funded by the Italian Department of Civil Protection within the project DPC-RELUIS 2016 - RS4 ''Seismic observatory of structures and health monitoring'' and by the "Centre of Integrated Geomorphology for the Mediterranean Area - CGIAM" within the Framework Agreement with the University of Basilicata "Study, Research and Experimentation in the Field of Analysis and Monitoring of Seismic Vulnerability of Strategic and Relevant Buildings for the purposes of Civil Protection and Development of Innovative Strategies of Seismic Reinforcement".

Impact of Fe(III)-OM complexes and Fe(III) polymerization on SOM pools reactivity under different land uses

NASA Astrophysics Data System (ADS)

Giannetta, B.; Plaza, C.; Zaccone, C.; Siebecker, M. G.; Rovira, P.; Vischetti, C.; Sparks, D. L.

2017-12-01

Soil organic matter (SOM) protection and long-term accumulation are controlled by adsorption to mineral surfaces in different ways, depending on its molecular structure and pedo-climatic conditions. Iron (Fe) oxides are known to be key regulators of the soil carbon (C) cycle, and Fe speciation in soils is highly dependent on environmental conditions and chemical interactions with SOM. However, the molecular structure and hydrolysis of Fe species formed in association with SOM is still poorly described. We hypothesize the existence of two pools of Fe which interact with SOM: mononuclear Fe(III)-SOM complexes and precipitated Fe(III) hydroxides. To verify our hypothesis, we investigated the interactions between Fe(III) and physically isolated soil fractions by means of batch experiments at pH 7. Specifically, we examined the fine silt plus clay (FSi+C) fraction, obtained by ultrasonic dispersion and wet sieving. The soil samples spanned several land uses, including coniferous forest (CFS), grassland (GS), technosols (TS) and agricultural (AS) soils. Solid phase products and supernatants were analyzed for C and Fe content. X-ray diffraction (XRD) and Brunauer-Emmett-Teller (BET) analysis were also performed. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to assess the main C functional groups involved in C complexation and desorption experiments. Preliminary linear combination fitting (LCF) of Fe K-edge extended X-ray absorption fine structure (EXAFS) spectra suggested the formation of ferrihydrite-like polymeric Fe(III) oxides in reacted CFS and GS samples, with higher C and Fe concentration. Conversely, mononuclear Fe(III) OM complexes dominated the speciation for TS and AS samples, characterized by lower C and Fe concentration, inhibiting the hydrolysis and polymerization of Fe (III). This approach will help revealing the mechanisms by which SOM pools can control Fe(III) speciation, and will elucidate how both Fe(III)-OM complexes and Fe(III) polymerization can affect SOM reactivity and, consequently, its mean residence time in different ecosystems.

BiodivERsA project VineDivers: Analysing interlinkages between soil biota and biodiversity-based ecosystem services in vineyards across Europe

NASA Astrophysics Data System (ADS)

Zaller, Johann G.; Winter, Silvia; Strauss, Peter; Querner, Pascal; Kriechbaum, Monika; Pachinger, Bärbel; Gómez, José A.; Campos, Mercedes; Landa, Blanca; Popescu, Daniela; Comsa, Maria; Iliescu, Maria; Tomoiaga, Liliana; Bunea, Claudiu-Ioan; Hoble, Adela; Marghitas, Liviu; Rusu, Teodor; Lora, Ángel; Guzmán, Gema; Bergmann, Holger

2015-04-01

Essential ecosystem services provided by viticultural landscapes result from diverse communities of above- and belowground organisms and their interactions. For centuries traditional viticulture was part of a multifunctional agricultural system including low-input grasslands and fruit trees resulting in a high functional biodiversity. However, in the last decades intensification and mechanisation of vineyard management caused a separation of production and conservation areas. As a result of management intensification including frequent tilling and/or use of pesticides several ecosystem services are affected leading to high rates of soil erosion, degradation of soil structure and fertility, contamination of groundwater and high levels of agricultural inputs. In this transdisciplinary BiodivERsA project we will examine to what extent differently intensive managed vineyards affect the activity and diversity of soil biota (e.g. earthworms, collembola, soil microorganisms) and how this feed back on aboveground biodiversity (e.g. weeds, pollinators). We will also investigate ecosystem services associated with soil faunal activity and biodiversity such as soil structure, the formation of stable soil aggregates, water infiltration, soil erosion as well as grape quality. These effects will become increasingly important as more extreme precipitation events are predicted with climate change. The socio-economic part of the project will investigate the role of diversely structured, species-rich viticultural landscapes as a cultural heritage providing aesthetic values for human well-being and recreation. The project objectives will be analysed at plot, field (vineyard) and landscape scales in vineyards located in Spain, France, Romania and Austria. A detailed engagement and dissemination plan for stakeholder at the different governance levels will accompany scientific research and will contribute to the implementation of best-practice recommendations for policy and farmers.

SITE AMPLIFICATION OF EARTHQUAKE GROUND MOTION.

USGS Publications Warehouse

Hays, Walter W.

1986-01-01

When analyzing the patterns of damage in an earthquake, physical parameters of the total earthquake-site-structure system are correlated with the damage. Soil-structure interaction, the cause of damage in many earthquakes, involves the frequency-dependent response of both the soil-rock column and the structure. The response of the soil-rock column (called site amplification) is controversial because soil has strain-dependent properties that affect the way the soil column filters the input body and surface seismic waves, modifying the amplitude and phase spectra and the duration of the surface ground motion.

Soil-pipe interaction modeling for pipe behavior prediction with super learning based methods

NASA Astrophysics Data System (ADS)

Shi, Fang; Peng, Xiang; Liu, Huan; Hu, Yafei; Liu, Zheng; Li, Eric

2018-03-01

Underground pipelines are subject to severe distress from the surrounding expansive soil. To investigate the structural response of water mains to varying soil movements, field data, including pipe wall strains in situ soil water content, soil pressure and temperature, was collected. The research on monitoring data analysis has been reported, but the relationship between soil properties and pipe deformation has not been well-interpreted. To characterize the relationship between soil property and pipe deformation, this paper presents a super learning based approach combining feature selection algorithms to predict the water mains structural behavior in different soil environments. Furthermore, automatic variable selection method, e.i. recursive feature elimination algorithm, were used to identify the critical predictors contributing to the pipe deformations. To investigate the adaptability of super learning to different predictive models, this research employed super learning based methods to three different datasets. The predictive performance was evaluated by R-squared, root-mean-square error and mean absolute error. Based on the prediction performance evaluation, the superiority of super learning was validated and demonstrated by predicting three types of pipe deformations accurately. In addition, a comprehensive understand of the water mains working environments becomes possible.

A multi-scale ''soil water structure'' model based on the pedostructure concept

NASA Astrophysics Data System (ADS)

Braudeau, E.; Mohtar, R. H.; El Ghezal, N.; Crayol, M.; Salahat, M.; Martin, P.

2009-02-01

Current soil water models do not take into account the internal organization of the soil medium and, a fortiori, the physical interaction between the water film surrounding the solid particles of the soil structure, and the surface charges of this structure. In that sense they empirically deal with the physical soil properties that are all generated from this soil water-structure interaction. As a result, the thermodynamic state of the soil water medium, which constitutes the local physical conditions, namely the pedo-climate, for biological and geo-chemical processes in soil, is not defined in these models. The omission of soil structure from soil characterization and modeling does not allow for coupling disciplinary models for these processes with soil water models. This article presents a soil water structure model, Kamel®, which was developed based on a new paradigm in soil physics where the hierarchical soil structure is taken into account allowing for defining its thermodynamic properties. After a review of soil physics principles which forms the basis of the paradigm, we describe the basic relationships and functionality of the model. Kamel® runs with a set of 15 soil input parameters, the pedohydral parameters, which are parameters of the physically-based equations of four soil characteristic curves that can be measured in the laboratory. For cases where some of these parameters are not available, we show how to estimate these parameters from commonly available soil information using published pedotransfer functions. A published field experimental study on the dynamics of the soil moisture profile following a pounded infiltration rainfall event was used as an example to demonstrate soil characterization and Kamel® simulations. The simulated soil moisture profile for a period of 60 days showed very good agreement with experimental field data. Simulations using input data calculated from soil texture and pedotransfer functions were also generated and compared to simulations of the more ideal characterization. The later comparison illustrates how Kamel® can be used and adapt to any case of soil data availability. As physically based model on soil structure, it may be used as a standard reference to evaluate other soil-water models and also pedotransfer functions at a given location or agronomical situation.

Centrifugal and Numerical Modeling of Buried Structures. Volume 2. Dynamic Soil-Structure Interaction.

DTIC Science & Technology

1987-07-14

RD-RISE 368 CENTRIFUGAL AND NUMERICAL MODELING OF BURIED STRUCTURES 1/3 VOLUME 2 DYNAMIC..(U) COLORADO UNIV AT BOULDER DEPT OF CIVIL ENVIRONMENTAL...20332-6448 ELEMENT NO NO. NO ACCESSION NO 61102F 2302 Cl 11 TITLE (Include Security Classification) (U) Centrifugal and Numerical Modeling of Buried ...were buried in a dry sand and tested in the centrifuge to simulate the effects of gravity-induced overburden stresses which played a major role in

Aspect has a greater impact on alpine soil bacterial community structure than elevation.

PubMed

Wu, Jieyun; Anderson, Barbara J; Buckley, Hannah L; Lewis, Gillian; Lear, Gavin

2017-03-01

Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Pesticide interactions with soils affected by olive oil mill wastewater

NASA Astrophysics Data System (ADS)

Keren, Yonatan; Bukhanovsky, Nadezhda; Borisover, Mikhail

2013-04-01

Soil pesticide sorption is well known to affect the fate of pesticides, their bioavailability and the potential to contaminate air and water. Soil - pesticide interactions may be strongly influenced by soil organic matter (SOM) and organic matter (OM)-rich soil amendments. One special OM source in soils is related to olive oil production residues that may include both solid and liquid wastes. In the Mediterranean area, the olive oil production is considered as an important field in the agricultural sector. Due to the significant rise in olive oil production, the amount of wastes is growing respectively. Olive oil mill waste water (OMWW) is the liquid byproduct in the so-called "three phase" technological process. Features of OMWW include the high content of fatty aliphatic components and polyphenols and their often-considered toxicity. One way of OMWW disposal is the land spreading, e.g., in olive orchards. The land application of OMWW (either controlled or not) is supposed to affect the multiple soil properties, including hydrophobicity and the potential of soils to interact with pesticides. Therefore, there is both basic and applied interest in elucidating the interactions between organic compounds and soils affected by OMWW. However, little is known about the impact of OMWW - soil interactions on sorption of organic compounds, and specifically, on sorption of agrochemicals. This paper reports an experimental study of sorption interactions of a series of organic compounds including widely used herbicides such as diuron and simazine, in a range of soils that were affected by OMWW (i) historically or (ii) in the controlled land disposal experiments. It is demonstrated that there is a distinct increase in apparent sorption of organic chemicals in soils affected by OMWW. In selected systems, this increase may be explained by increase in SOM content. However, the SOM quality places a role: the rise in organic compound - soil interactions may both exceed the SOM content increase and be less than that. Sorption interactions of herbicides with soils demonstrate a strong hysteresis (which is not expected to be related to a biodegradation). The data suggests that the OMWW - soil interaction seems to change the shape of the apparent sorption isotherms of organic sorbates, and, possibly, their sorption mechanisms: from a Langmuir-like sorption isotherm (describing the adsorptive interactions with a saturation of sorption sites) in the native soils to the sigmoidal or linear isotherms (expected for a partitioning into the bulk OM phases and their swelling) in the OMWW-amended soils. These results may have a significant impact on multiple agricultural and hydrological aspects, e.g., such as the application rate of herbicides in the field, and their possible release and the long term effect on groundwater. The authors acknowledge the support from the OLIVEOIL project (SCHA849/13) funded by DFG.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kennedy, R.P.; Kincaid, R.H.; Short, S.A.

This report presents the results of part of a two-task study on the engineering characterization of earthquake ground motion for nuclear power plant design. Task I of the study, which is presented in NUREG/CR-3805, Vol. 1, developed a basis for selecting design response spectra taking into account the characteristics of free-field ground motion found to be significant in causing structural damage. Task II incorporates additional considerations of effects of spatial variations of ground motions and soil-structure interaction on foundation motions and structural response. The results of Task II are presented in four parts: (1) effects of ground motion characteristics onmore » structural response of a typical PWR reactor building with localized nonlinearities and soil-structure interaction effects; (2) empirical data on spatial variations of earthquake ground motion; (3) soil-structure interaction effects on structural response; and (4) summary of conclusions and recommendations based on Tasks I and II studies. This report presents the results of the first part of Task II. The results of the other parts will be presented in NUREG/CR-3805, Vols. 3 to 5.« less

Interactions between soil texture, water, and nutrients control patterns of biocrusts abundance and structure

NASA Astrophysics Data System (ADS)

Young, Kristina; Bowker, Matthew; Reed, Sasha; Howell, Armin

2017-04-01

Heterogeneity in the abiotic environment structures biotic communities by controlling niche space and parameters. This has been widely observed and demonstrated in vascular plant and other aboveground communities. While soil organisms are presumably also strongly influenced by the physical and chemical dimensions of the edaphic environment, there are fewer studies linking the development, structure, productivity or function of surface soil communities to specific edaphic gradients. Here, we use biological soil crusts (biocrusts) as a model system to determine mechanisms regulating community structure of soil organisms. We chose soil texture to serve as an edaphic gradient because of soil texture's influence over biocrust distribution on a landscape level. We experimentally manipulated texture in constructed soil, and simultaneously manipulated two main outcomes of texture, water and nutrient availability, to determine the mechanism underlying texture's influence on biocrust abundance and structure. We grew biocrust communities from a field-sourced inoculum on four different soil textures, sieved from the same parent soil material, manipulating watering levels and nutrient additions across soil textures in a full-factorial design over a 5-month period of time. We measured abundance and structure of biocrusts over time, and measured two metrics of function, N2 fixation rates and soil stabilization, at the conclusion of the experiment. Our results showed finer soil textures resulted in faster biocrust community development and dominance by mosses, whereas coarser textures grew more slowly and had biocrust communities dominated by cyanobacteria and lichen. Additionally, coarser textured soils contained cyanobacterial filaments significantly deeper into the soil profile than fine textured soils. N2-fixation values increased with increasing moss cover and decreased with increasing cyanobacterial cover, however, the rate of change depended on soil texture and water amount. Soil shear resistance was highest on finer textured soil with the highest watering treatment, whereas compression resistance was highest on the coarsest textured soils with the highest watering amounts. Nutrient addition did not influence total cover or biocrust function, but did decrease lichen cover. Taken together, these results suggest that interactions between soil texture, water, and to a lesser degree nutrients, create predictable patterns in biocrust assemblage and offers a mechanistic understanding of edaphic controls over biocrust abundance and structure. These insights add to our increasing understanding of how edaphic gradients structure soil communities.

Constraining soil C cycling with strategic, adaptive action for data and model reporting

NASA Astrophysics Data System (ADS)

Harden, J. W.; Swanston, C.; Hugelius, G.

2015-12-01

Regional to global carbon assessments include a variety of models, data sets, and conceptual structures. This includes strategies for representing the role and capacity of soils to sequester, release, and store carbon. Traditionally, many soil carbon data sets emerged from agricultural missions focused on mapping and classifying soils to enhance and protect production of food and fiber. More recently, soil carbon assessments have allowed for more strategic measurement to address the functional and spatially explicit role that soils play in land-atmosphere carbon exchange. While soil data sets are increasingly inter-comparable and increasingly sampled to accommodate global assessments, soils remain poorly constrained or understood with regard to their role in spatio-temporal variations in carbon exchange. A more deliberate approach to rapid improvement in our understanding involves a community-based activity than embraces both a nimble data repository and a dynamic structure for prioritization. Data input and output can be transparent and retrievable as data-derived products, while also being subjected to rigorous queries for merging and harmonization into a searchable, comprehensive, transparent database. Meanwhile, adaptive action groups can prioritize data and modeling needs that emerge through workshops, meta-data analyses or model testing. Our continual renewal of priorities should address soil processes, mechanisms, and feedbacks that significantly influence global C budgets and/or significantly impact the needs and services of regional soil resources that are impacted by C management. In order to refine the International Soil Carbon Network, we welcome suggestions for such groups to be led on topics such as but not limited to manipulation experiments, extreme climate events, post-disaster C management, past climate-soil interactions, or water-soil-carbon linkages. We also welcome ideas for a business model that can foster and promote idea and data sharing.

Beech cupules as keystone structures for soil fauna.

PubMed

Melguizo-Ruiz, Nereida; Jiménez-Navarro, Gerardo; Moya-Laraño, Jordi

2016-01-01

Facilitative or positive interactions are ubiquitous in nature and play a fundamental role in the configuration of ecological communities. In particular, habitat modification and niche construction, in which one organism locally modifies abiotic conditions and favours other organisms by buffering the effects of adverse environmental factors, are among the most relevant facilitative interactions. In line with this, 'keystone structures', which provide resources, refuge, or advantageous services decisive for other species, may allow the coexistence of various species and thus considerably contribute to diversity maintenance. Beech cupules are woody husks harbouring beech fruits that remain in the forest soil for relatively long periods of time. In this study, we explored the potential role of these cupules in the distribution and maintenance of the soil fauna inhabiting the leaf litter layer. We experimentally manipulated cupule availability and soil moisture in the field to determine if such structures are limiting and can provide moist shelter to soil animals during drought periods, contributing to minimize desiccation risks. We measured invertebrate abundances inside relative to outside the cupules, total abundances in the leaf litter and animal body sizes, in both dry and wet experimental plots. We found that these structures are preferentially used by the most abundant groups of smaller soil animals-springtails, mites and enchytraeids-during droughts. Moreover, beech cupules can be limiting, as an increase in use was found with higher cupule densities, and are important resources for many small soil invertebrates, driving the spatial structure of the soil community and promoting higher densities in the leaf litter, probably through an increase in habitat heterogeneity. We propose that fruit woody structures should be considered 'keystone structures' that contribute to soil community maintenance. Therefore, beech trees may indirectly facilitate soil fauna activities through their decaying fruit husks, hence acting as ecosystem engineers.

Ecohydrologic processes and soil thickness feedbacks control limestone-weathering rates in a karst landscape

DOE PAGES

Dong, Xiaoli; Cohen, Matthew J.; Martin, Jonathan B.; ...

2018-05-18

Here, chemical weathering of bedrock plays an essential role in the formation and evolution of Earth's critical zone. Over geologic time, the negative feedback between temperature and chemical weathering rates contributes to the regulation of Earth climate. The challenge of understanding weathering rates and the resulting evolution of critical zone structures lies in complicated interactions and feedbacks among environmental variables, local ecohydrologic processes, and soil thickness, the relative importance of which remains unresolved. We investigate these interactions using a reactive-transport kinetics model, focusing on a low-relief, wetland-dominated karst landscape (Big Cypress National Preserve, South Florida, USA) as a case study.more » Across a broad range of environmental variables, model simulations highlight primary controls of climate and soil biological respiration, where soil thickness both supplies and limits transport of biologically derived acidity. Consequently, the weathering rate maximum occurs at intermediate soil thickness. The value of the maximum weathering rate and the precise soil thickness at which it occurs depend on several environmental variables, including precipitation regime, soil inundation, vegetation characteristics, and rate of groundwater drainage. Simulations for environmental conditions specific to Big Cypress suggest that wetland depressions in this landscape began to form around beginning of the Holocene with gradual dissolution of limestone bedrock and attendant soil development, highlighting large influence of age-varying soil thickness on weathering rates and consequent landscape development. While climatic variables are often considered most important for chemical weathering, our results indicate that soil thickness and biotic activity are equally important. Weathering rates reflect complex interactions among soil thickness, climate, and local hydrologic and biotic processes, which jointly shape the supply and delivery of chemical reactants, and the resulting trajectories of critical zone and karst landscape development.« less

Ecohydrologic processes and soil thickness feedbacks control limestone-weathering rates in a karst landscape

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Xiaoli; Cohen, Matthew J.; Martin, Jonathan B.

Here, chemical weathering of bedrock plays an essential role in the formation and evolution of Earth's critical zone. Over geologic time, the negative feedback between temperature and chemical weathering rates contributes to the regulation of Earth climate. The challenge of understanding weathering rates and the resulting evolution of critical zone structures lies in complicated interactions and feedbacks among environmental variables, local ecohydrologic processes, and soil thickness, the relative importance of which remains unresolved. We investigate these interactions using a reactive-transport kinetics model, focusing on a low-relief, wetland-dominated karst landscape (Big Cypress National Preserve, South Florida, USA) as a case study.more » Across a broad range of environmental variables, model simulations highlight primary controls of climate and soil biological respiration, where soil thickness both supplies and limits transport of biologically derived acidity. Consequently, the weathering rate maximum occurs at intermediate soil thickness. The value of the maximum weathering rate and the precise soil thickness at which it occurs depend on several environmental variables, including precipitation regime, soil inundation, vegetation characteristics, and rate of groundwater drainage. Simulations for environmental conditions specific to Big Cypress suggest that wetland depressions in this landscape began to form around beginning of the Holocene with gradual dissolution of limestone bedrock and attendant soil development, highlighting large influence of age-varying soil thickness on weathering rates and consequent landscape development. While climatic variables are often considered most important for chemical weathering, our results indicate that soil thickness and biotic activity are equally important. Weathering rates reflect complex interactions among soil thickness, climate, and local hydrologic and biotic processes, which jointly shape the supply and delivery of chemical reactants, and the resulting trajectories of critical zone and karst landscape development.« less

The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry.

PubMed

Liu, Shanshan; Wang, Feng; Xue, Kai; Sun, Bo; Zhang, Yuguang; He, Zhili; Van Nostrand, Joy D; Zhou, Jizhong; Yang, Yunfeng

2015-03-01

Soil transplant into warmer regions has been shown to alter soil microbiology. In contrast, little is known about the effects of soil transplant into colder regions, albeit that climate cooling has solicited attention in recent years. To address this question, we transplanted bare fallow soil over large transects from southern China (subtropical climate zone) to central (warm temperate climate zone) and northern China (cold temperate climate zone). After an adaptation period of 4 years, soil nitrogen components, microbial biomass and community structures were altered. However, the effects of soil transplant on microbial communities were dampened by maize cropping, unveiling a negative interaction between cropping and transplant. Further statistical analyses with Canonical correspondence analysis and Mantel tests unveiled annual average temperature, relative humidity, aboveground biomass, soil pH and NH4 (+) -N content as environmental attributes closely correlated with microbial functional structures. In addition, average abundances of amoA-AOA (ammonia-oxidizing archaea) and amoA-AOB (ammonia-oxidizing bacteria) genes were significantly (P < 0.05) correlated with soil nitrification capacity, hence both AOA and AOB contributed to the soil functional process of nitrification. These results suggested that the soil nitrogen cycle was intimately linked with microbial community structure, and both were subjected to disturbance by soil transplant to colder regions and plant cropping. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Plant-soil interactions promote co-occurrence of three nonnative woody shrubs.

PubMed

Kuebbing, Sara E; Classen, Aimée T; Call, Jaime J; Henning, Jeremiah A; Simberloff, Daniel

2015-08-01

Ecosystems containing multiple nonnative plant species are common, but mechanisms promoting their co-occurrence are understudied. Plant-soil interactions contribute to the dominance of singleton species in nonnative ranges because many nonnatives experience stronger positive feedbacks relative to co-occurring natives. Plant-soil interactions could impede other nonnatives if an individual nonnative benefits from its soil community to a greater extent than its neighboring nonnatives, as is seen with natives. However, plant-soil interactions could promote nonnative co-occurrence if a nonnative accumulates beneficial soil mutualists that also assist other nonnatives. Here, we use greenhouse and field experiments to ask whether plant-soil interactions (1) promote the codominance of two common nonnative shrubs (Ligustrum sinense and Lonicera maackii) and (2) facilitate the invasion of a less-common nonnative shrub (Rhamnus davurica) in deciduous forests of the southeastern United States. In the greenhouse, we found that two of the nonnatives, L. maackii and R. davurica, performed better in soils conditioned by nonnative shrubs compared to uninvaded forest soils, which. suggests that positive feedbacks among co-occurring nonnative shrubs can promote continued invasion of a site. In both greenhouse and field experiments, we found consistent signals that the codominance of the nonnatives L. sinense and L. maackii may be at least partially explained by the increased growth of L. sinense in L. maackii soils. Overall, significant effects of plant-soil interactions on shrub performance indicate that plant-soil interactions can potentially structure the co-occurrence patterns of these nonnatives.

Composite Behavior of Geosynthetic Reinforced Soil Mass

DOT National Transportation Integrated Search

2013-07-01

This study investigated the composite behavior of a geosynthetic reinforced soil (GRS) mass. Many studies have been conducted on the behavior of GRS structures; however, the interactive behavior between the soil and geosynthetic reinforcement in a GR...

Estimating Vegetation Structure in African Savannas using High Spatial Resolution Imagery

NASA Astrophysics Data System (ADS)

Axelsson, C.; Hanan, N. P.

2016-12-01

High spatial resolution satellite imagery allows for detailed mapping of trees in savanna landscapes, including estimates of woody cover, tree densities, crown sizes, and the spatial pattern of trees. By linking these vegetation parameters to rainfall and soil properties we gain knowledge of how the local environment influences vegetation. A thorough understanding of the underlying ecosystem processes is key to assessing the future productivity and stability of these ecosystems. In this study, we have processed and analyzed hundreds of sites sampled from African savannas across a wide range of rainfall and soil conditions. The vegetation at each site is classified using unsupervised classification with manual assignment into woody, herbaceous and bare cover classes. A crown delineation method further divides the woody areas into individual tree crowns. The results show that rainfall, soil, and topography interactively influence vegetation structure. We see that both total rainfall and rainfall seasonality play important roles and that soil type influences woody cover and the sizes of tree crowns.

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest.

PubMed

Schilling, Erik M; Waring, Bonnie G; Schilling, Jonathan S; Powers, Jennifer S

2016-09-01

We investigated how forest composition, litter quality, and rainfall interact to affect leaf litter decomposition across three successional tropical dry forests in Costa Rica. We monitored litter stocks and bulk litter turnover in 18 plots that exhibit substantial variation in soil characteristics, tree community structure, fungal communities (including forests dominated by ecto- or arbuscular mycorrhizal host trees), and forest age. Simultaneously, we decomposed three standard litter substrates over a 6-month period spanning an unusually intense drought. Decay rates of standard substrates depended on the interaction between litter identity and forest type. Decomposition rates were correlated with tree and soil fungal community composition as well as soil fertility, but these relationships differed among litter types. In low fertility soils dominated by ectomycorrhizal oak trees, bulk litter turnover rates were low, regardless of soil moisture. By contrast, in higher fertility soils that supported mostly arbuscular mycorrhizal trees, bulk litter decay rates were strongly dependent on seasonal water availability. Both measures of decomposition increased with forest age, as did the frequency of termite-mediated wood decay. Taken together, our results demonstrate that soils and forest age exert strong control over decomposition dynamics in these tropical dry forests, either directly through effects on microclimate and nutrients, or indirectly by affecting tree and microbial community composition and traits, such as litter quality.

Radioisotope tracer approach for understanding the impacts of global change-induced pedoturbation on soil C dynamics

NASA Astrophysics Data System (ADS)

Gonzalez-Meler, M. A.; Sturchio, N. C.; Sanchez-de Leon, Y.; Blanc-Betes, E.; Taneva, L.; Poghosyan, A.; Norby, R. J.; Filley, T. R.; Guilderson, T. P.; Welker, J. M.

2010-12-01

Biogeochemical carbon-cycle feedbacks to climate are apparent but uncertain, primarily because of gaps in mechanistic understanding on the ecosystem processes that drive carbon cycling and storage in terrestrial ecosystems, particularly in soils. Recent findings are increasingly recognizing the interaction between soil biota and the soil physical environment. Soil carbon turnover is partly determined by burial of organic matter and its physical and chemical protection. These factors are potentially affected by changes in climate (freezing-thawing or wet-drying cycles) or ecosystem structure including biological invasions. A major impediment to understanding dynamics of soil C in terrestrial systems is our inability to measure soil physical processes such as soil mixing rates or turnover of soil structures, including aggregates. Here we present a multiple radioisotope tracer approach (naturally occurring and man-made) to measure soil mixing rates in response to global change. We will present evidence of soil mixing rate changes in a temperate forest exposed to increased levels of atmospheric CO2 and in a tundra ecosystem exposed to increased thermal insulation. In both cases, radioisotope tracers proved to be an effective way to measure effects of global change on pedoturbation. Results also provided insights into the specific mechanisms involved in the responses. Elevated CO2 resulted in deeper soil mixing cells (increased by about 5cm on average) when compared to control soils as a consequence of changes in biota (increased root growth, higher earthworm density). In the tundra, soil warming induced higher rates of cryoturbation, resulting in what appears to be a net uplift of organic matter to the surface thereby exposing deeper C to decomposers. In both cases, global change factors affected the vertical distribution of C and changed the amount of bulk soil actively involved in soil processes. As a consequence, comparisons of C budgets to a given soil depth in response to global change factors may be misleading if they do not account for the depth change in the soil mixing cells.

Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation.

PubMed

Sun, Weimin; Li, Jiwei; Jiang, Lei; Sun, Zhilei; Fu, Meiyan; Peng, Xiaotong

2015-10-01

Successful bioremediation of oil pollution is based on a comprehensive understanding of the in situ physicochemical conditions and indigenous microbial communities as well as the interaction between microorganisms and geochemical variables. Nineteen oil-contaminated soil samples and five uncontaminated controls were taken from six major oilfields across different geoclimatic regions in China to investigate the spatial distribution of the microbial ecosystem. Microbial community analysis revealed remarkable variation in microbial diversity between oil-contaminated soils taken from different oilfields. Canonical correspondence analysis (CCA) further demonstrated that a suite of in situ geochemical parameters, including soil moisture and sulfate concentrations, were among the factors that influenced the overall microbial community structure and composition. Phylogenetic analysis indicated that the vast majority of sequences were related to the genera Arthrobacter, Dietzia, Pseudomonas, Rhodococcus, and Marinobacter, many of which contain known oil-degrading or oil-emulsifying species. Remarkably, a number of archaeal genera including Halalkalicoccus, Natronomonas, Haloterrigena, and Natrinema were found in relatively high abundance in some of the oil-contaminated soil samples, indicating that these Euryarchaeota may play an important ecological role in some oil-contaminated soils. This study offers a direct and reliable reference of the diversity of the microbial community in various oil-contaminated soils and may influence strategies for in situ bioremediation of oil pollution.

A new model for humic materials and their interactions with hydrophobic organic chemicals in soil-water or sediment-water systems

USGS Publications Warehouse

Wershaw, R. L.

1986-01-01

A generalized model of humic materials in soils and sediments, which is consistent with their observed properties, is presented. This model provides a means of understanding the interaction of hydrophobic pollutants with humic materials. In this model, it is proposed that the humic materials in soils and sediments consist of a number of different oligomers and simple compounds which result from the partial degradation of plant remains. These degradation products are stabilized by incorporation into humic aggregates bound together by weak bonding mechanisms, such as hydrogen bonding, pi bonding, and hydrophobic interactions. The resulting structures are similar to micelles or membranes, in which the interiors of the structures are hydrophobic and the exteriors are hydrophilic. Hydrophobic compounds will partition into the hydrophobic interiors of the humic micelles or "membrane-like" structures. ?? 1986.

Heathlands confronting global change: drivers of biodiversity loss from past to future scenarios

PubMed Central

Fagúndez, Jaime

2013-01-01

Background Heathlands are dynamic plant communities characterized by a high cover of sclerophyllous, ericoid shrubs that develop over nutrient-poor soils. Interest in the preservation of these habitats in Europe has increased over the last decades, but over this time there has been a general decline in habitat quality, affecting community structure, ecosystem functions and biodiversity. Negative drivers that trigger these changes include land-use changes (i.e. habitat destruction and fragmentation), pollution, climate change, natural succession and human management, as well as the presence of invasive exotic species. Scope Based on recent scientific literature, the effect of each of these potential drivers on a wide set of factors, including physiological traits, species richness and diversity, community structure, ecosystem functions and soil conditions, is reviewed. The effects of these drivers are generally understood, but the direction and magnitude of factor interactions, whenever studied, have shown high variability. Conclusions Habitat loss and fragmentation affect sensitive species and ecosystem functions. The nature of the surrounding area will condition the quality of the heathland remnants by, for example, propagule pressure from invasive species. The dominant ericoid shrubs can be out-competed by vigorous perennial grasses with increased atmospheric nitrogen deposition, although interactions with climate and management practices may either counteract or enhance this process. Grazing or periodic burning promotes heath loss but site-specific combined treatments maintain species diversity and community structure. Climate change alone moderately affects plant diversity, community structure and ecosystem functions. Combined with other factors, climatic changes will condition heath development, mainly with regard to key aspects such as seed set and seedling establishment, rare species occurrence and nutrient cycling in the soil. It is essential to address the effects of not only individual factors, but their interactions, together with land-use history, on heathland development and conservation in order to predict habitat response to future scenarios. PMID:23223202

Heathlands confronting global change: drivers of biodiversity loss from past to future scenarios.

PubMed

Fagúndez, Jaime

2013-02-01

Heathlands are dynamic plant communities characterized by a high cover of sclerophyllous, ericoid shrubs that develop over nutrient-poor soils. Interest in the preservation of these habitats in Europe has increased over the last decades, but over this time there has been a general decline in habitat quality, affecting community structure, ecosystem functions and biodiversity. Negative drivers that trigger these changes include land-use changes (i.e. habitat destruction and fragmentation), pollution, climate change, natural succession and human management, as well as the presence of invasive exotic species. Based on recent scientific literature, the effect of each of these potential drivers on a wide set of factors, including physiological traits, species richness and diversity, community structure, ecosystem functions and soil conditions, is reviewed. The effects of these drivers are generally understood, but the direction and magnitude of factor interactions, whenever studied, have shown high variability. Habitat loss and fragmentation affect sensitive species and ecosystem functions. The nature of the surrounding area will condition the quality of the heathland remnants by, for example, propagule pressure from invasive species. The dominant ericoid shrubs can be out-competed by vigorous perennial grasses with increased atmospheric nitrogen deposition, although interactions with climate and management practices may either counteract or enhance this process. Grazing or periodic burning promotes heath loss but site-specific combined treatments maintain species diversity and community structure. Climate change alone moderately affects plant diversity, community structure and ecosystem functions. Combined with other factors, climatic changes will condition heath development, mainly with regard to key aspects such as seed set and seedling establishment, rare species occurrence and nutrient cycling in the soil. It is essential to address the effects of not only individual factors, but their interactions, together with land-use history, on heathland development and conservation in order to predict habitat response to future scenarios.

Small-scale barriers mitigate desertification processes and enhance plant recruitment in a degraded semiarid grassland

USGS Publications Warehouse

Fick, Stephen E; Decker, Cheryl E.; Duniway, Michael C.; Miller, Mark E.

2016-01-01

Anthropogenic desertification is a problem that plagues drylands globally; however, the factors which maintain degraded states are often unclear. In Canyonlands National Park on the Colorado Plateau of southeastern Utah, many degraded grasslands have not recovered structure and function >40 yr after release from livestock grazing pressure, necessitating active restoration. We hypothesized that multiple factors contribute to the persistent degraded state, including lack of seed availability, surficial soil-hydrological properties, and high levels of spatial connectivity (lack of perennial vegetation and other surface structure to retain water, litter, seed, and sediment). In combination with seeding and surface raking treatments, we tested the effect of small barrier structures (“ConMods”) designed to disrupt the loss of litter, seed and sediment in degraded soil patches within the park. Grass establishment was highest when all treatments (structures, seed addition, and soil disturbance) were combined, but only in the second year after installation, following favorable climatic conditions. We suggest that multiple limiting factors were ameliorated by treatments, including seed limitation and microsite availability, seed removal by harvester ants, and stressful abiotic conditions. Higher densities of grass seedlings on the north and east sides of barrier structures following the summer months suggest that structures may have functioned as artificial “nurse-plants”, sheltering seedlings from wind and radiation as well as accumulating wind-blown resources. Barrier structures increased the establishment of both native perennial grasses and exotic annuals, although there were species-specific differences in mortality related to spatial distribution of seedlings within barrier structures. The unique success of all treatments combined, and even then only under favorable climatic conditions and in certain soil patches, highlights that restoration success (and potentially, natural regeneration) often is contingent on many interacting factors.

Assessing agricultural management effects on structure related soil hydraulic properties by tension infiltrometry

NASA Astrophysics Data System (ADS)

Bodner, G.; Loiskandl, W.; Kaul, H.-P.

2009-04-01

Soil structure is a dynamic property subject to numerous natural and human influences. It is recognized as fundamental for sustainable functioning of soil. Therefore knowledge of management impacts on the sensitive structural states of soil is decisive in order to avoid soil degradation. The stabilization of the soil's (macro)pore system and eventually the improvement of its infiltrability are essential to avoid runoff and soil erosion, particularly in view of an increasing probability of intense rainfall events. However structure-related soil properties generally have a high natural spatiotemporal variability that interacts with the potential influence of agricultural land use. This complicates a clear determination of management vs. environmental effects and requires adequate measurement methods, allowing a sufficient spatiotemporal resolution to estimate the impact of the targeted management factors within the natural dynamics of soil structure. A common method to assess structure-related soil hydraulic properties is tension infiltrometry. A major advantage of tension infiltrometer measurements is that no or only minimum soil disturbance is necessary and several structure-controlled water transmission properties can readily be derived. The method is more time- and cost-efficient compared to laboratory measurements of soil hydraulic properties, thus enabling more replications. Furthermore in situ measurements of hydraulic properties generally allow a more accurate reproduction of field soil water dynamics. The present study analyses the impact of two common agricultural management options on structure related hydraulic properties based on tension infiltrometer measurements. Its focus is the identification of the role of management within the natural spatiotemporal variability, particularly in respect to seasonal temporal dynamics. Two management approaches are analysed, (i) cover cropping as a "plant-based" agro-environmental measure, and (ii) tillage with different intensities including conventional tillage with a mouldboard plough, reduced tillage with a chisel plough and no-tillage. The results showed that the plant-based management measure of cover cropping had only minor influence on near-saturated hydraulic conductivity (kh) and flow weighted mean pore radius (λm). Substantial over-winter changes were found with a significant increase in kh and a reduction in the pore radius. A spatial trend in soil texture along the cover cropped slope resulted in a higher kh at lower pressure heads at the summit with higher fractions of coarse particles, while kh tended to be highest at the toeslope towards saturation. Cover crop management accounted for a maximum of 9.7% of the total variability in kh, with a decreasing impact towards the unsaturated range. A substantial difference to bare soil in the cover cropped treatments could be identified in relation to a stabilization of macro-pores over winter. The different tillage treatments had a substantial impact on near-saturated kh and pore radius. Although conventional tillage showed the highest values in kh and λm, settling of the soil after the ploughing event tended to reduce differences over time compared to the other tillage methods. The long-term no-tillage (10 years) however had the lowest values of kh at all measurement dates. The high contents of silt and fine sand probably resulted in soil densification that was not counterbalanced sufficiently by biological structure forming agents. The study could show that soil structure related hydraulic properties are subject to a substantial seasonal variability. A comprehensive assessment of agricultural measures such as tillage or cover cropping requires an estimate of these temporal dynamics and their interaction with the management strategies. Particularly for plant-based management measures such as cover cropping, which represent a less intense intervention in the structural states of the soil compared to tillage, this was evident, as the main mechanism revealed for this measure was structure stabilization over time. While spatial variability is mostly controlled in designed experiments, the role of temporal variability is often underestimated. From our study we concluded that (i) a proper understanding of processes involved in management effects on soil structure must take into consideration the dynamic nature of the respective soil properties, (ii) experimental planning for studies regarding management impacts on soil structure should allow an estimation of temporal variability, and (iii) for this purpose tension infiltrometry provides an efficient measurement tool to assess structure related soil hydraulic properties.

Effect of antecedent terrestrial land-use on C and N cycling in created wetlands

NASA Astrophysics Data System (ADS)

McCalley, C. K.; Al Graiti, T.; Williams, T.; Huang, S.; McGowan, M. B.; Eddingsaas, N. C.; Tyler, A. C.

2017-12-01

Land-use legacies and their interaction with both management actions and climate variability has a poorly characterized impact on the development of ecosystem functions and the trajectory of climate-carbon feedbacks. The complex structure-function relationships in wetlands foster delivery of valuable, climate sensitive, ecosystem services (carbon sequestration, nutrient removal, flood control, etc.) but also make them susceptible to colonization by invasive plants and lead to emission of key greenhouse gases. This project uses created wetland ecosystems as a model to understand how heterogeneity in antecedent conditions interacts with management options to create unique structure-function scenarios and a range of climate feedback outcomes. We utilized ongoing experiments in created wetlands that differ in antecedent conditions (crop agriculture, livestock grazing) and investigated how management options (invasive species removal, organic matter addition) interact with legacy impacts to promote key ecosystem functions, including greenhouse gas emissions, carbon sequestration, denitrification and plant biodiversity. The effects of antecedent land-use on soil chemistry, coupled with hydrologic patterns resulted in wetlands with divergent C and N dynamics despite their similar creation history. Additionally, the occurrence of extreme weather events (drought and excessive flooding) during the study period highlighted the overarching role that increased climate variability will play in determining key ecosystem processes in wetlands. Responses to management were linked to hydro-period: while organic matter addition successfully increased soil organic matter to more closely replicate natural systems at all sites, it had the largest impact on C and N cycling when soils were saturated. Overall, environmental conditions that promoted saturated soils, both those shaped by human activities or climate extremes, enhanced primary productivity, nutrient removal and greenhouse gas production as well as decreased soil respiration.

Surface soil root response to season of repeated fire in a young longleaf pine plantation

Treesearch

Mary Anne Sword Sayer; James D. Haywood

2012-01-01

The potential exists for interaction between naturally high soil bulk density and low soil water content to create root-growth limiting soil strengths. This problem is commonly remedied by soil structural attributes, old root channels and other perturbations, and periods of wetness during which soil strength is favorable for root elongation. Because the application and...

The transformation of weak saturated soils using piles-drains for improving its mechanical properties

NASA Astrophysics Data System (ADS)

Ter-Martirosyan, Z. G.; Ter-Martirosyan, A. Z.; Sidorov, V. V.

2018-04-01

In practice of increased responsibility structures design there are often weak saturated clayey soils with low characteristics of deformability and strength take place on the construction site. In these cases, foundations using piles-drains of sandy or coarse material are recommended by norms, which is able to bear the load and to accelerate the consolidation process. The presented solutions include an analytical solution of the interaction problem between piles and slab raft foundation with the surrounding soil of the base with the possibility of extension of pile shaft. The closed-form solutions to determine the stresses in pile shaft and in the soil under the foundation slab are obtained. The article presents the results of large scale tests in the pilot area construction of major energy facilities in Russia.

Bridge-in-a-Backpack(TM). Task 2.3 : low-rise arch study with soil-structure interaction and spread footing foundation.

DOT National Transportation Integrated Search

2015-01-01

This report includes fulfillment of Task 2.3 of a multi-task contract to further enhance concrete filled FRP tubes, or : the Bridge in a Backpack. Task 2 is an investigation of alternative shapes for the FRP tubes with varying radii. Task : 2.3 explo...

Are preferential flow paths perpetuated by microbial activity in the soil matrix? A review

NASA Astrophysics Data System (ADS)

Morales, Verónica L.; Parlange, J.-Yves; Steenhuis, Tammo S.

2010-10-01

SummaryRecently, the interactions between soil structure and microbes have been associated with water transport, retention and preferential or column flow development. Of particular significance is the potential impact of microbial extracellular polymeric substances (EPS) on soil porosity (i.e., hydraulic conductivity reduction or bioclogging) and of exudates from biota, including bacteria, fungi, roots and earthworms on the degree of soil water repellency. These structural and surface property changes create points of wetting instability, which under certain infiltrating conditions can often result in the formation of persistent preferential flow paths. Moreover, distinct differences in physical and chemical properties between regions of water flow (preferential flow paths) and no-flow (soil matrix) provide a unique set of environmental living conditions for adaptable microorganisms to exist. In this review, special consideration is given to: (1) the functional significance of microbial activity in the host porous medium in terms of feedback mechanisms instigated by irregular water availability and (2) the related physical and chemical conditions that force the organization and formation of unique microbial habitats in unsaturated soils that prompt and potentially perpetuate the formation of preferential flow paths in the vadose zone.

Modelling of deformation of underground tunnel lining, interacting with water-saturated soil

NASA Astrophysics Data System (ADS)

Berezhnoi, D. V.; Balafendieva, I. S.; Sachenkov, A. A.; Sekaeva, L. R.

2016-11-01

Built finite element method of calculating the deformation of underground tunnel lining, interacting with dry and water-saturated soils. To simulate the interaction between the lining and soils environments, including physical and non-linear, a special "contact" finite element, which allows to consider all cases of interaction between the contacting surfaces. It solved a number of problems of deformation with the ground subway tunnel lining rings.

Response analysis of a nuclear containment structure with nonlinear soil-structure interaction under bi-directional ground motion

NASA Astrophysics Data System (ADS)

Kumar, Santosh; Raychowdhury, Prishati; Gundlapalli, Prabhakar

2015-06-01

Design of critical facilities such as nuclear power plant requires an accurate and precise evaluation of seismic demands, as any failure of these facilities poses immense threat to the community. Design complexity of these structures reinforces the necessity of a robust 3D modeling and analysis of the structure and the soil-foundation interface. Moreover, it is important to consider the multiple components of ground motion during time history analysis for a realistic simulation. Present study is focused on investigating the seismic response of a nuclear containment structure considering nonlinear Winkler-based approach to model the soil-foundation interface using a distributed array of inelastic springs, dashpots and gap elements. It is observed from this study that the natural period of the structure increases about 10 %, whereas the force demands decreases up to 24 % by considering the soil-structure interaction. Further, it is observed that foundation deformations, such as rotation and sliding are affected by the embedment ratio, indicating an increase of up to 56 % in these responses for a reduction of embedment from 0.5 to 0.05× the width of the footing.

Phylogenetic structure of soil bacterial communities predicts ecosystem functioning.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Verdú, Miguel

2015-05-01

Quantifying diversity with phylogeny-informed metrics helps understand the effects of diversity on ecosystem functioning (EF). The sign of these effects remains controversial because phylogenetic diversity and taxonomic identity may interactively influence EF. Positive relationships, traditionally attributed to complementarity effects, seem unimportant in natural soil bacterial communities. Negative relationships could be attributed to fitness differences leading to the overrepresentation of few productive clades, a mechanism recently invoked to assemble soil bacteria communities. We tested in two ecosystems contrasting in terms of environmental heterogeneity whether two metrics of phylogenetic community structure, a simpler measure of phylogenetic diversity (NRI) and a more complex metric incorporating taxonomic identity (PCPS), correctly predict microbially mediated EF. We show that the relationship between phylogenetic diversity and EF depends on the taxonomic identity of the main coexisting lineages. Phylogenetic diversity was negatively related to EF in soils where a marked fertility gradient exists and a single and productive clade (Proteobacteria) outcompete other clades in the most fertile plots. However, phylogenetic diversity was unrelated to EF in soils where the fertility gradient is less marked and Proteobacteria coexist with other abundant lineages. Including the taxonomic identity of bacterial lineages in metrics of phylogenetic community structure allows the prediction of EF in both ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Annual grass invasion in sagebrush-steppe: The relative importance of climate, soil properties and biotic interactions

USGS Publications Warehouse

Bansal, Sheel; Sheley, Roger L.

2016-01-01

The invasion by winter-annual grasses (AGs) such as Bromus tectorum into sagebrush steppe throughout the western USA is a classic example of a biological invasion with multiple, interacting climate, soil and biotic factors driving the invasion, although few studies have examined all components together. Across a 6000-km2 area of the northern Great Basin, we conducted a field assessment of 100 climate, soil, and biotic (functional group abundances, diversity) factors at each of 90 sites that spanned an invasion gradient ranging from 0 to 100 % AG cover. We first determined which biotic and abiotic factors had the strongest correlative relationships with AGs and each resident functional group. We then used regression and structural equation modeling to explore how multiple ecological factors interact to influence AG abundance. Among biotic interactions, we observed negative relationships between AGs and biodiversity, perennial grass cover, resident species richness, biological soil crust cover and shrub density, whereas perennial and annual forb cover, tree cover and soil microbial biomass had no direct linkage to AG. Among abiotic factors, AG cover was strongly related to climate (increasing cover with increasing temperature and aridity), but had weak relationships with soil factors. Our structural equation model showed negative effects of perennial grasses and biodiversity on AG cover while integrating the negative effects of warmer climate and positive influence of belowground processes on resident functional groups. Our findings illustrate the relative importance of biotic interactions and climate on invasive abundance, while soil properties appear to have stronger relationships with resident biota than with invasives.

How to examine soil sorption of ionizable organic compounds and avoid varying pH?

NASA Astrophysics Data System (ADS)

Borisover, Mikhail

2017-04-01

Multiple natural and anthropogenic organic compounds including new and emerging pollutants undergo ionization in aqueous solutions, and their sorption by soils and sediments is contributed by presence of both molecular and ionized species. Better understanding of environmental fate of organic chemicals requires taking into account interactions of molecular and ionized species with environmental sorbents. A "standard" (and undoubtedly important) procedure for differentiating contributions of molecular and ionized species into the overall soil sorption of an organic compound involves varying pH of solution in batch sorption experiments. However, varying pH is (1) often not possible, without destroying a sorbent, e.g., due to the buffer capacity of soils containing carbonates, (2) difficult for further interpretation, since it changes not only the ionization status of a solute in a solution but also the sorbent structure, e.g., a conformation of organic matter, and/or ionization of surface functional groups, (3) making difficult (or even impossible) to explicitly evaluate the role of dissolved species-bulk water interactions, directly affecting the affinity of a sorbate to distribute between water and a sorbent. Indeed, both molecular and ionized species undergo interactions with the solvent bulk and, at least in the case of the ionized ones, there was no a simple way to quantify organic ion-water interactions and their role in organic ion distribution between soil and water phases. This paper presents a "counter-intuitive" approach to examine sorption interactions of an ionizable compound, without experimenting with varied pH. The approach is based on an idea of replacing an initial state in sorption transfer of an ionizable compound from the solvent bulk to a solvated (hydrated) sorbed state: a traditional coefficient describing distribution of a partially ionized compound between a hydrated sorbent and a co-equilibrated aqueous phase is converted to the coefficient describing the transfer of the sorbing compound from its initial molecular (non-ionized) state (in a solution or in the gas phase) to the final hydrated sorbed state equilibrated with the actual aqueous solution of this ionizable compound. In this way, any contributions from the bulk solvent-organic ion interactions into the sorption transfer may be excluded; in addition, further any solute-solvent interactions may be taken out of the consideration. Therefore, compound's sorption characteristics "cleared" of solute-solvent interactions may be obtained, and a better understanding of relations between interactions in a sorbed phase and a molecular structure of organic sorbates can be reached. The approach is illustrated by examining sorption of variously ionized organic compounds, i.e., those belonging to the pharmaceuticals and personal care products (triclosan, gemfibrozil, galaxolide), and aliphatic organic acids on natural and organic amendment-enriched soils. Specifically, it is demonstrated how the greater H-donating ability of trifluoroacetic acid, as compared with acetic acid, strengthens the acid interactions in the soil phase. In another series of examples, it is shown how hydrophobic and non-ionizing galaxolide interacts weakly with soils, as compared with partially ionized triclosan and almost fully ionized gemfibrozil, i.e., leading to the conclusions not reachable based only on the direct comparison of experimentally measured distribution coefficients.

Using Plant Phylogenetic Relatedness as a Predictor for Plants' Control on Soil Microbial Communities and Nitrogen Cycling

NASA Astrophysics Data System (ADS)

Potter, T.; Bowman, W. D.

2016-12-01

Despite the known importance of soil microbes and their influence on soil processes, a mechanistic understanding is still needed to predict how plants and soil microbes interact at scales that are relevant to community and ecosystem-scale processes. Closely related plant species have similar traits aboveground, but we don't know whether this is also true for belowground traits that affect soil microbial community structure and function. Determining how tightly plant phylogeny and plant functional traits are linked to soil microbial communities is a useful approach for discovering plant-microbe associations that are generalizable across plant species (a limitation of studies that employ a single or few plant species). Using this approach, we conducted a greenhouse study with seven congeneric grasses (genus Poa) and their native soils to examine whether plants' influences on microbial community structure were consistent with plant phylogenetic relatedness and/or plant functional traits. Seeds of each Poa species were planted in native soil (from the seed source population) as well as a homogenized soil from all seven populations. Additionally, a nitrogen treatment was added to address how an environmental change (such as nitrogen deposition) alters plant-microbe associations. Rhizosphere community composition of bacteria and fungi was obtained via marker gene sequencing to compare community composition across plant species. Patterns in plant-microbe associations across plant species reveal plant control on nutrient cycling via plant species' influence on microbial community structure. These results determine if we are ready to generalize about plant-microbe interactions at the genus level, an important stepping-stone to applying knowledge of plant-microbe interactions to larger ecological scales.

Modelling fungal growth in heterogeneous soil: analyses of the effect of soil physical structure on fungal community dynamics

NASA Astrophysics Data System (ADS)

Falconer, R.; Radoslow, P.; Grinev, D.; Otten, W.

2009-04-01

Fungi play a pivital role in soil ecosystems contributing to plant productivity. The underlying soil physical and biological processes responsible for community dynamics are interrelated and, at present, poorly understood. If these complex processes can be understood then this knowledge can be managed with an aim to providing more sustainable agriculture. Our understanding of microbial dynamics in soil has long been hampered by a lack of a theoretical framework and difficulties in observation and quantification. We will demonstrate how the spatial and temporal dynamics of fungi in soil can be understood by linking mathematical modelling with novel techniques that visualise the complex structure of the soil. The combination of these techniques and mathematical models opens up new possibilities to understand how the physical structure of soil affects fungal colony dynamics and also how fungal dynamics affect soil structure. We will quantify, using X ray tomography, soil structure for a range of artificially prepared microcosms. We characterise the soil structures using soil metrics such as porosity, fractal dimension, and the connectivity of the pore volume. Furthermore we will use the individual based fungal colony growth model of Falconer et al. 2005, which is based on the physiological processes of fungi, to assess the effect of soil structure on microbial dynamics by qualifying biomass abundances and distributions. We demonstrate how soil structure can critically affect fungal species interactions with consequences for biological control and fungal biodiversity.

Shaping an Optimal Soil by Root-Soil Interaction.

PubMed

Jin, Kemo; White, Philip J; Whalley, William R; Shen, Jianbo; Shi, Lei

2017-10-01

Crop production depends on the availability of water and mineral nutrients, and increased yields might be facilitated by a greater focus on roots-soil interactions. Soil properties affecting plant growth include drought, compaction, nutrient deficiency, mineral toxicity, salinity, and submergence. Plant roots respond to the soil environment both spatially and temporally by avoiding stressful soil environments and proliferating in more favorable environments. We observe that crops can be bred for specific root architectural and biochemical traits that facilitate soil exploration and resource acquisition, enabling greater crop yields. These root traits affect soil physical and chemical properties and might be utilized to improve the soil for subsequent crops. We argue that optimizing root-soil interactions is a prerequisite for future food security. Copyright © 2017 Elsevier Ltd. All rights reserved.

Critical Zone Co-dynamics: Quantifying Interactions between Subsurface, Land Surface, and Vegetation Properties Using UAV and Geophysical Approaches

NASA Astrophysics Data System (ADS)

Dafflon, B.; Leger, E.; Peterson, J.; Falco, N.; Wainwright, H. M.; Wu, Y.; Tran, A. P.; Brodie, E.; Williams, K. H.; Versteeg, R.; Hubbard, S. S.

2017-12-01

Improving understanding and modelling of terrestrial systems requires advances in measuring and quantifying interactions among subsurface, land surface and vegetation processes over relevant spatiotemporal scales. Such advances are important to quantify natural and managed ecosystem behaviors, as well as to predict how watershed systems respond to increasingly frequent hydrological perturbations, such as droughts, floods and early snowmelt. Our study focuses on the joint use of UAV-based multi-spectral aerial imaging, ground-based geophysical tomographic monitoring (incl., electrical and electromagnetic imaging) and point-scale sensing (soil moisture sensors and soil sampling) to quantify interactions between above and below ground compartments of the East River Watershed in the Upper Colorado River Basin. We evaluate linkages between physical properties (incl. soil composition, soil electrical conductivity, soil water content), metrics extracted from digital surface and terrain elevation models (incl., slope, wetness index) and vegetation properties (incl., greenness, plant type) in a 500 x 500 m hillslope-floodplain subsystem of the watershed. Data integration and analysis is supported by numerical approaches that simulate the control of soil and geomorphic characteristic on hydrological processes. Results provide an unprecedented window into critical zone interactions, revealing significant below- and above-ground co-dynamics. Baseline geophysical datasets provide lithological structure along the hillslope, which includes a surface soil horizon, underlain by a saprolite layer and the fractured Mancos shale. Time-lapse geophysical data show very different moisture dynamics in various compartments and locations during the winter and growing season. Integration with aerial imaging reveals a significant linkage between plant growth and the subsurface wetness, soil characteristics and the topographic gradient. The obtained information about the organization and connectivity of the landscape is being transferred to larger regions using aerial imaging and will be used to constrain multi-scale, multi-physics hydro-biogeochemical simulations of the East River watershed response to hydrological perturbations.

A dynamic organic soil biogeochemical model for simulating the effects of wildfire on soil environmental conditions and carbon dynamics of black spruce forests

Treesearch

Shuhua Yi; A. David McGuire; Eric Kasischke; Jennifer Harden; Kristen Manies; Michelle Mack; Merritt Turetsky

2010-01-01

Ecosystem models have not comprehensively considered how interactions among fire disturbance, soil environmental conditions, and biogeochemical processes affect ecosystem dynamics in boreal forest ecosystems. In this study, we implemented a dynamic organic soil structure in the Terrestrial Ecosystem Model (DOS-TEM) to investigate the effects of fire on soil temperature...

Soil macroinvertebrate communities across a productivity gradient in deciduous forests of eastern North America

Treesearch

Evelyn S. Wenk; Mac A. Callaham; Joseph O' Brien; Paul J. Hanson

2016-01-01

Within the temperate, deciduous forests of the eastern US, diverse soil-fauna communities are structured by a combination of environmental gradients and interactions with other biota. The introduction of non-native soil taxa has altered communities and soil processes, and adds another degree of variability to these systems. We sampled soil macroinvertebrate abundance...

Elucidating the Physical and Chemical Structural Changes of Proteins on Clay Mineral Surfaces using Large-scale Molecular Dynamics Simulations in Tandem with NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Washton, N.; Reardon, P.; Chacon, S. S.; Burton, S.; Lipton, A.; Kleber, M.; Qafoku, N. P.

2014-12-01

Carbon cycling among the three major Earth's pools, i.e., atmosphere, terrestrial systems and oceans, has received increased attention because the concentration of CO2 in the atmosphere has increased significantly in recent years reaching concentrations greater than 400 ppm that have never been recorded before, warming the planet and changing the climate. Within the terrestrial system, soil organic matter (SOM) represents an important sub-pool of carbon. The associations of SOM with soil mineral interfaces and particles, creating micro-aggregates, are believed to regulate the bioavailability of the associated organic carbon by protecting it from transformations and mineralization to carbon dioxide. Nevertheless, the molecular scale interactions of different types of SOM with a variety of soil minerals and the controls on the extent and rate of SOM transformation and mineralization are not well documented in the current literature. Given the importance of SOM fate and persistence in soils and the current knowledge gaps, the application of atomistic scale simulations to study SOM/mineral associations in abiotic model systems offers rich territory for original and impactful science. Molecular modeling and simulation of SOM is a burgeoning and challenging avenue for aiding the characterization of these complex compounds and chemical systems and for studying their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types and common in soils, which are thought to contribute to their reactive properties including recalcitrance potential and resistance to mineralization. Here, we will discuss our large-scale molecular dynamics simulation efforts to explore the interaction of proteins with clay minerals (i.e., phyllosilicates such as kaolinite, smectite and micas), including the potential physical and chemical structural changes of proteins, protein adsorption by polar and permanently charged mineral surfaces and variably charged edges, and the potential role of amphiphilic proteins in providing adsorptive layers for SOM-mineral interfaces. Our efforts at characterizing these systems through combined modeling and simulation and NMR will also be discussed.

[Understory effects on overstory trees: A review.

PubMed

Du, Zhong; Cai, Xiao Hu; Bao, Wei Kai; Chen, Huai; Pan, Hong Li

2016-03-01

Plant-plant interactions play a key role in regulating the composition and structure of communities and ecosystems. Studies of plant-plant interactions in forest ecosystems have traditionally concentrated on either tree-tree interactions or overstory species' impacts on understory plants. The possible effects of understory species on overstory trees have received less attention. We summarized the effects of understory species on soil physiological properties, soil fauna activities, leaf litter decomposition, and ecophysiology and growth of the overstory species. Then the effects of distur-bance on understory-overstory interactions were discussed. Finally, an ecophysiology-based concept model of understory effects on overstory trees was proposed. Understory removal experiments showed that the study area, overstory species age, soil fertility and understory species could significantly affect the understory-overstory interactions.

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

PubMed

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Structural and seismic analyses of waste facility reinforced concrete storage vaults

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, C.Y.

1995-07-01

Facility 317 of Argonne National Laboratory consists of several reinforced concrete waste storage vaults designed and constructed in the late 1940`s through the early 1960`s. In this paper, structural analyses of these concrete vaults subjected to various natural hazards are described, emphasizing the northwest shallow vault. The natural phenomenon hazards considered include both earthquakes and tornados. Because these vaults are deeply embedded in the soil, the SASSI (System Analysis of Soil-Structure Interaction) code was utilized for the seismic calculations. The ultimate strength method was used to analyze the reinforced concrete structures. In all studies, moment and shear strengths at criticalmore » locations of the storage vaults were evaluated. Results of the structural analyses show that almost all the waste storage vaults meet the code requirements according to ACI 349--85. These vaults also satisfy the performance goal such that confinement of hazardous materials is maintained and functioning of the facility is not interrupted.« less

Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

NASA Technical Reports Server (NTRS)

Noor, A. K. (Editor); Hayduk, R. J. (Editor)

1985-01-01

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

An investigation into the reactions of biochar in soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joseph, Stephen; Camps-Arbestain, Marta; Lin, Yun

2010-10-12

Interactions between biochar, soil, microbes and plant roots may occur within a short period of time after application to the soil. The extent, rates and implications of these interactions, however, are far from being understood. This review includes a description of the properties of biochars and suggests possible reactions that may occur after the addition of biochars to soil. These include dissolution-precipitation, adsorption-desorption, acid-base and redox reactions. Special attention is given to reactions occurring within pores, and to interactions with roots, microorganisms and soil fauna. The examination of biochars (from chicken litter, greenwaste and paper mill sludges) weathered for onemore » and two years in an Australian Ferrosol provides evidence for some of the mechanisms described in this review and offers an insight to reactions at a molecular scale. These interactions are biochar- and site-specific. Therefore, suitable experimental trials combining biochar types and different pedoclimatic conditions are needed to determine the extent to which these reactions influence the potential of biochar as a soil amendment and C-sequestration tool.« less

Impacts of manganese mining activity on the environment: interactions among soil, plants, and arbuscular mycorrhiza.

PubMed

Rivera-Becerril, Facundo; Juárez-Vázquez, Lucía V; Hernández-Cervantes, Saúl C; Acevedo-Sandoval, Otilio A; Vela-Correa, Gilberto; Cruz-Chávez, Enrique; Moreno-Espíndola, Iván P; Esquivel-Herrera, Alfonso; de León-González, Fernando

2013-02-01

The mining district of Molango in the Hidalgo State, Mexico, possesses one of the largest deposits of manganese (Mn) ore in the world. This research assessed the impacts of Mn mining activity on the environment, particularly the interactions among soil, plants, and arbuscular mycorrhiza (AM) at a location under the influence of an open Mn mine. Soils and plants from three sites (soil under maize, soil under native vegetation, and mine wastes with some vegetation) were analyzed. Available Mn in both soil types and mine wastes did not reach toxic levels. Samples of the two soil types were similar regarding physical, chemical, and biological properties; mine wastes were characterized by poor physical structure, nutrient deficiencies, and a decreased number of arbuscular mycorrhizal fungi (AMF) spores. Tissues of six plant species accumulated Mn at normal levels. AM was absent in the five plant species (Ambrosia psilostachya, Chenopodium ambrosoides, Cynodon dactylon, Polygonum hydropiperoides, and Wigandia urens) established in mine wastes, which was consistent with the significantly lower number of AMF spores compared with both soil types. A. psilostachya (native vegetation) and Zea mays showed mycorrhizal colonization in their root systems; in the former, AM significantly decreased Mn uptake. The following was concluded: (1) soils, mine wastes, and plant tissues did not accumulate Mn at toxic levels; (2) despite its poor physical structure and nutrient deficiencies, the mine waste site was colonized by at least five plant species; (3) plants growing in both soil types interacted with AMF; and (4) mycorrhizal colonization of A. psilostachya influenced low uptake of Mn by plant tissues.

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling

PubMed Central

Wang, Feng; Liang, Yuting; Jiang, Yuji; Yang, Yunfeng; Xue, Kai; Xiong, Jinbo; Zhou, Jizhong; Sun, Bo

2015-01-01

Plants have an important impact on soil microbial communities and their functions. However, how plants determine the microbial composition and network interactions is still poorly understood. During a four-year field experiment, we investigated the functional gene composition of three types of soils (Phaeozem, Cambisols and Acrisol) under maize planting and bare fallow regimes located in cold temperate, warm temperate and subtropical regions, respectively. The core genes were identified using high-throughput functional gene microarray (GeoChip 3.0), and functional molecular ecological networks (fMENs) were subsequently developed with the random matrix theory (RMT)-based conceptual framework. Our results demonstrated that planting significantly (P < 0.05) increased the gene alpha-diversity in terms of richness and Shannon – Simpson’s indexes for all three types of soils and 83.5% of microbial alpha-diversity can be explained by the plant factor. Moreover, planting had significant impacts on the microbial community structure and the network interactions of the microbial communities. The calculated network complexity was higher under maize planting than under bare fallow regimes. The increase of the functional genes led to an increase in both soil respiration and nitrification potential with maize planting, indicating that changes in the soil microbial communities and network interactions influenced ecological functioning. PMID:26396042

Effects of interactions between Collembola and soil microbial community on the degradation of glyphosate-based herbicide

NASA Astrophysics Data System (ADS)

Wee, J.; Lee, Y. S.; Son, J.; Kim, Y.; Nam, T. H.; Cho, K.

2017-12-01

Glyphosate is the most widely used herbicide because of its broad spectrum activity and effectiveness, however, little is known about adverse effects on non-target species and their interactions. Therefore, in this study, we investigated the effects of glyphosate on interactions between Collembola and soil microbial community and the effect of Collembola on degradation of glyphosate. The experiment carried out in PS container filled with 30g of soil according to OECD 232 guidelines. Investigating the effects of soil microbial community and Collembola on degradation of glyphosate, we prepared defaunated field soil (only maintaining soil microbial community, sampling in May and September, 2016.) and autoclaved soil with 0, 10, 30 adults of Paronychiurus kimi (Collembola) respectively. Survived adults and hatched juveniles of P. kimi were counted after 28-day exposures in both soils spiked with 100 mg/kg of glyphosate. Glyphosate in soil of 7, 14, 21, 28 days after spiking of glyphosate based herbicide was analyzed by spectrophotometer (Jan et al., 2009). Also soil microbial community structure was investigated using phospholipid fatty acids (PLFAs) composition analysis of soils following the procedures given by the Sherlock Microbial Identification System (MIDI Inc., Newark, DE). Glyphosate (100mg/kg soil) has no effects on reproduction and survival of P. kimi in any soils. Also, glyphosate in soils with Collembola was more rapidly degraded. Rapid increase of soil microbial biomass(PLFAs) was shown in soil with Collembola addition. This result showed that glyphosate affected interactions between Collembola and soil microorganisms, and also soil microbial community affected by Collembola changed degradation of glyphosate.

Belowground rhizomes in paleosols: The hidden half of an Early Devonian vascular plant

NASA Astrophysics Data System (ADS)

Xue, Jinzhuang; Deng, Zhenzhen; Huang, Pu; Huang, Kangjun; Benton, Michael J.; Cui, Ying; Wang, Deming; Liu, Jianbo; Shen, Bing; Basinger, James F.; Hao, Shougang

2016-08-01

The colonization of terrestrial environments by rooted vascular plants had far-reaching impacts on the Earth system. However, the belowground structures of early vascular plants are rarely documented, and thus the plant-soil interactions in early terrestrial ecosystems are poorly understood. Here we report the earliest rooted paleosols (fossil soils) in Asia from Early Devonian deposits of Yunnan, China. Plant traces are extensive within the soil and occur as complex network-like structures, which are interpreted as representing long-lived, belowground rhizomes of the basal lycopsid Drepanophycus. The rhizomes produced large clones and helped the plant survive frequent sediment burial in well-drained soils within a seasonal wet-dry climate zone. Rhizome networks contributed to the accumulation and pedogenesis of floodplain sediments and increased the soil stabilizing effects of early plants. Predating the appearance of trees with deep roots in the Middle Devonian, plant rhizomes have long functioned in the belowground soil ecosystem. This study presents strong, direct evidence for plant-soil interactions at an early stage of vascular plant radiation. Soil stabilization by complex rhizome systems was apparently widespread, and contributed to landscape modification at an earlier time than had been appreciated.

Belowground rhizomes in paleosols: The hidden half of an Early Devonian vascular plant.

PubMed

Xue, Jinzhuang; Deng, Zhenzhen; Huang, Pu; Huang, Kangjun; Benton, Michael J; Cui, Ying; Wang, Deming; Liu, Jianbo; Shen, Bing; Basinger, James F; Hao, Shougang

2016-08-23

The colonization of terrestrial environments by rooted vascular plants had far-reaching impacts on the Earth system. However, the belowground structures of early vascular plants are rarely documented, and thus the plant-soil interactions in early terrestrial ecosystems are poorly understood. Here we report the earliest rooted paleosols (fossil soils) in Asia from Early Devonian deposits of Yunnan, China. Plant traces are extensive within the soil and occur as complex network-like structures, which are interpreted as representing long-lived, belowground rhizomes of the basal lycopsid Drepanophycus The rhizomes produced large clones and helped the plant survive frequent sediment burial in well-drained soils within a seasonal wet-dry climate zone. Rhizome networks contributed to the accumulation and pedogenesis of floodplain sediments and increased the soil stabilizing effects of early plants. Predating the appearance of trees with deep roots in the Middle Devonian, plant rhizomes have long functioned in the belowground soil ecosystem. This study presents strong, direct evidence for plant-soil interactions at an early stage of vascular plant radiation. Soil stabilization by complex rhizome systems was apparently widespread, and contributed to landscape modification at an earlier time than had been appreciated.

Belowground rhizomes in paleosols: The hidden half of an Early Devonian vascular plant

PubMed Central

Xue, Jinzhuang; Deng, Zhenzhen; Huang, Pu; Huang, Kangjun; Benton, Michael J.; Cui, Ying; Wang, Deming; Liu, Jianbo; Shen, Bing; Basinger, James F.; Hao, Shougang

2016-01-01

The colonization of terrestrial environments by rooted vascular plants had far-reaching impacts on the Earth system. However, the belowground structures of early vascular plants are rarely documented, and thus the plant−soil interactions in early terrestrial ecosystems are poorly understood. Here we report the earliest rooted paleosols (fossil soils) in Asia from Early Devonian deposits of Yunnan, China. Plant traces are extensive within the soil and occur as complex network-like structures, which are interpreted as representing long-lived, belowground rhizomes of the basal lycopsid Drepanophycus. The rhizomes produced large clones and helped the plant survive frequent sediment burial in well-drained soils within a seasonal wet−dry climate zone. Rhizome networks contributed to the accumulation and pedogenesis of floodplain sediments and increased the soil stabilizing effects of early plants. Predating the appearance of trees with deep roots in the Middle Devonian, plant rhizomes have long functioned in the belowground soil ecosystem. This study presents strong, direct evidence for plant−soil interactions at an early stage of vascular plant radiation. Soil stabilization by complex rhizome systems was apparently widespread, and contributed to landscape modification at an earlier time than had been appreciated. PMID:27503883

Influence of humic substances and iron and aluminum ions on the sorption of acetamiprid to an arable soil.

PubMed

Murano, Hirotatsu; Suzuki, Katsuhiro; Kayada, Saori; Saito, Mitsuhiko; Yuge, Naoya; Arishiro, Takuji; Watanabe, Akira; Isoi, Toshiyuki

2018-02-15

Humic substances (HS) in soil and sediments, and surface water influence the behavior of organic xenobiotics in the environment. However, our knowledge of the effects of specific HS fractions, i.e., humic acids (HAs), fulvic acids (FAs), and humin (HM), on the sorption of organic xenobiotics is limited. The neonicotinoid insecticide acetamiprid is thought to contribute to the collapse of honeybee colonies. To understand the role that soil organic matter plays in the fate of acetamiprid, interactions between acetamiprid and the above HS fractions were examined. Batch experiments were conducted using various combinations of a field soil sample and the above 3 HS fractions prepared from the same soil, and differences in isotherm values for acetamiprid sorption were investigated based on the structural differences among the HS fractions. The sorption of acetamiprid to soil minerals associated with HM (MHM) (Freundlich isotherm constant, K f : 6.100) was reduced when HAs or FAs were added (K f : 4.179 and 4.756, respectively). This can be attributed to hydrophobic interactions between HM and HAs or FAs in which their dissociated carboxyl and phenolic groups become oriented to face the soil solution. The amount of acetamiprid that was adsorbed to (MHM+HA) or (MHM+FA) increased when aluminum ions were added (K f : 6.933 and 10.48, respectively), or iron ions were added (K f : 7.303 and 11.29, respectively). Since acetamiprid has no affinity for inorganic components in soil, the formation of HS-metal complexes by cation bridging may have oriented the hydrophobic moieties in the HAs or FAs to face the soil solution and may also have resulted in the formation of dense structures, resulting in an increase in the amount of acetamiprid that becomes adsorbed to these structures. These results highlight the importance of interactions among soil components in the pedospheric diffusion of acetamiprid. Copyright © 2017 Elsevier B.V. All rights reserved.

Pull-out testing facility for geosynthetics.

DOT National Transportation Integrated Search

1992-11-01

The considerable increase in using geosynthetics in soil reinforcement made it necessary to develop methods of measuring the interaction properties and modeling load transfer in reinforced-soil structures. The large number of factors that influence t...

Agrophysical assessment of alluvial calcareous soils of the Çumra region of Central Anatolia in Turkey

NASA Astrophysics Data System (ADS)

Shein, E. V.; Erol, S. A.; Milanovskii, E. Yu.; Verkhovtseva, N. V.; Mikayilov, F. D.; Er, F.; Ersahin, S.

2014-07-01

Some physical (density, coefficient of filtration, particle-size composition, etc.) and chemical (contents of carbonates, organic carbon, nitrogen, etc.) properties of an alluvial calcareous soil were studied in Central Anatolia (Konya province, Çumra region). These heavy-textured (medium clay) soils with a low content of organic carbon (less than 1%) have favorable agrophysical properties due to the stable structure of the pore space. The studies of the water regime of soils under drop irrigation confirm the favorable hydrological properties of these soils. The use of the known agrophysical estimates (after Medvedev, the index of the optimal water regime, etc.) has revealed the high dispersal of the data related to the low humus content in these heavy-textured soils. The favorable structure of the pore space is suggested to be stipulated by the active activity of the numerous and diverse representatives of soil biota. Four phyla predominate in the microbio-logical composition of the soils studied; among them, Actinobacteria is the dominant. The composition of this phylum is dominated by the elevated number of both higher ( Streptomyces) and lower (three species of Rhodococcus) actinobacteria. The high biodiversity of bacteria against the background of their great total number and the developed trophic interactions in the microbial community promote the well-balanced production of specific metabolites, including gaseous ones (CO2, H2). This circumstance allows this clayey soil to function rather actively while protecting the pore space against compaction and maintaining the optimal density, porosity, and hydrological properties.

Uncovering trophic positions and food resources of soil animals using bulk natural stable isotope composition.

PubMed

Potapov, Anton M; Tiunov, Alexei V; Scheu, Stefan

2018-06-19

Despite the major importance of soil biota in nutrient and energy fluxes, interactions in soil food webs are poorly understood. Here we provide an overview of recent advances in uncovering the trophic structure of soil food webs using natural variations in stable isotope ratios. We discuss approaches of application, normalization and interpretation of stable isotope ratios along with methodological pitfalls. Analysis of published data from temperate forest ecosystems is used to outline emerging concepts and perspectives in soil food web research. In contrast to aboveground and aquatic food webs, trophic fractionation at the basal level of detrital food webs is large for carbon and small for nitrogen stable isotopes. Virtually all soil animals are enriched in 13 C as compared to plant litter. This 'detrital shift' likely reflects preferential uptake of 13 C-enriched microbial biomass and underlines the importance of microorganisms, in contrast to dead plant material, as a major food resource for the soil animal community. Soil organic matter is enriched in 15 N and 13 C relative to leaf litter. Decomposers inhabiting mineral soil layers therefore might be enriched in 15 N resulting in overlap in isotope ratios between soil-dwelling detritivores and litter-dwelling predators. By contrast, 13 C content varies little between detritivores in upper litter and in mineral soil, suggesting that they rely on similar basal resources, i.e. little decomposed organic matter. Comparing vertical isotope gradients in animals and in basal resources can be a valuable tool to assess trophic interactions and dynamics of organic matter in soil. As indicated by stable isotope composition, direct feeding on living plant material as well as on mycorrhizal fungi is likely rare among soil invertebrates. Plant carbon is taken up predominantly by saprotrophic microorganisms and channelled to higher trophic levels of the soil food web. However, feeding on photoautotrophic microorganisms and non-vascular plants may play an important role in fuelling soil food webs. The trophic niche of most high-rank animal taxa spans at least two trophic levels, implying the use of a wide range of resources. Therefore, to identify trophic species and links in food webs, low-rank taxonomic identification is required. Despite overlap in feeding strategies, stable isotope composition of the high-rank taxonomic groups reflects differences in trophic level and in the use of basal resources. Different taxonomic groups of predators and decomposers are likely linked to different pools of organic matter in soil, suggesting different functional roles and indicating that trophic niches in soil animal communities are phylogenetically structured. During last two decades studies using stable isotope analysis have elucidated the trophic structure of soil communities, clarified basal food resources of the soil food web and revealed links between above- and belowground ecosystem compartments. Extending the use of stable isotope analysis to a wider range of soil-dwelling organisms, including microfauna, and a larger array of ecosystems provides the perspective of a comprehensive understanding of the structure and functioning of soil food webs. © 2018 Cambridge Philosophical Society.

Effect of Humic Acids and pesticides on Agricultural Soil Structure and Stability and Its Implication on Soil Quality

NASA Astrophysics Data System (ADS)

Gaonkar, O. D.; Nambi, I. M.; G, S. K.

2016-12-01

The functional and morphological aspects of soil structure determine the soil quality. The dispersion of colloidal soil particles, especially the clay fraction and rupture of soil aggregates, both of which play an important role in soil structure development, lead to degradation of soil quality. The main objective of this work was to determine the effect of behaviour of soil colloids on the agricultural soil structure and quality. The effect of commercial humic acid, organophosphate pesticides and soil natural organic matter on the electrical and structural properties of the soil colloids was also studied. Agricultural soil, belonging to the sandy loam texture class from northern part of India was considered in this study. In order to understand the changes in the soil quality in the presence and absence of humic acids, the soil fabric and structure was analyzed by X-ray diffraction (XRD), Fourier Transform Infrared (FTIR) Spectroscopy and Scanning Electron Microscopy (SEM). Electrical properties of natural soil colloids in aqueous suspensions were assessed by zeta potential measurements at varying pH values with and without the presence of humic acids and pesticides. The influence of natural organic matter was analyzed by oxidizing the natural soil organic matter with hydrogen peroxide. The zeta potential of the soil colloids was found to be negative in the pH range studied. The results indicated that hydrogen peroxide treatment lead to deflocculation of colloidal soil particles. In addition, the humic acids undergoes effective adsorption onto the soil surface imparting more negative zeta potential to the colloidal soil particles. The soil hydrophilicity decreased in the presence of humic acids which was confirmed by surface free energy determination. Thus, it can be concluded that the presence of humic acids altered the soil fabric and structure, thereby affecting the soil quality. This study assumes significance in understanding the soil aggregation and the interactions at soil solid-liquid interface.

An analysis of transient flow in upland watersheds: interactions between structure and process

Treesearch

David Lawrence Brown

1995-01-01

The physical structure and hydrological processes of upland watersheds interact in response to forcing functions such as rainfall, leading to storm runoff generation and pore pressure evolution. Transient fluid flow through distinct flow paths such as the soil matrix, macropores, saprolite, and bedrock may be viewed as a consequence of such interactions. Field...

Methods, Computational Platform, Verification, and Application of Earthquake-Soil-Structure-Interaction Modeling and Simulation

NASA Astrophysics Data System (ADS)

Tafazzoli, Nima

Seismic response of soil-structure systems has attracted significant attention for a long time. This is quite understandable with the size and the complexity of soil-structure systems. The focus of three important aspects of ESSI modeling could be on consistent following of input seismic energy and a number of energy dissipation mechanisms within the system, numerical techniques used to simulate dynamics of ESSI, and influence of uncertainty of ESSI simulations. This dissertation is a contribution to development of one such tool called ESSI Simulator. The work is being done on extensive verified and validated suite for ESSI Simulator. Verification and validation are important for high fidelity numerical predictions of behavior of complex systems. This simulator uses finite element method as a numerical tool to obtain solutions for large class of engineering problems such as liquefaction, earthquake-soil-structure-interaction, site effect, piles, pile group, probabilistic plasticity, stochastic elastic-plastic FEM, and detailed large scale parallel models. Response of full three-dimensional soil-structure-interaction simulation of complex structures is evaluated under the 3D wave propagation. Domain-Reduction-Method is used for applying the forces as a two-step procedure for dynamic analysis with the goal of reducing the large size computational domain. The issue of damping of the waves at the boundary of the finite element models is studied using different damping patterns. This is used at the layer of elements outside of the Domain-Reduction-Method zone in order to absorb the residual waves coming out of the boundary layer due to structural excitation. Extensive parametric study is done on dynamic soil-structure-interaction of a complex system and results of different cases in terms of soil strength and foundation embedment are compared. High efficiency set of constitutive models in terms of computational time are developed and implemented in ESSI Simulator. Efficiency is done based on simplifying the elastic-plastic stiffness tensor of the constitutive models. Almost in all the soil-structure systems, there are interface zones in contact with each other. These zones can get detached during the loading or can slip on each other. In this dissertation the frictional contact element is implemented in ESSI Simulator. Extended verification has been done on the implemented element. The interest here is the effect of slipping and gap opening at the interface of soil and concrete foundation on the soil-structure system behavior. In fact transferring the loads to structure is defined based on the contact areas which will affect the response of the system. The effect of gap openings and sliding at the interfaces are shown through application examples. In addition, dissipation of the seismic energy due to frictional sliding of the interface zones are studied. Application Programming Interface (API) and Domain Specific Language (DSL) are being developed to increase developer's and user's modeling and simulation capabilities. API describes software services developed by developers that are used by users. A domain-specific language (DSL) is a small language which usually focuses on a particular problem domain in software. In general DSL programs are translated to a common function or library which can be viewed as a tool to hide the details of the programming, and make it easier for the user to deal with the commands.

Salt marsh-mangrove ecotones: using structural gradients to investigate the effects of woody plant encroachment on plant-soil interactions and ecosystem carbon pools

USGS Publications Warehouse

Yando, Erik S.; Osland, Michael J.; Willis, Jonathan M; Day, Richard H.; Krauss, Ken W.; Hester, Mark W.

2016-01-01

Synthesis: Our results indicate that the ecological implications of woody plant encroachment in tidal saline wetlands are dependent upon precipitation controls of plant–soil interactions. Although the above-ground effects of mangrove expansion are consistently large, below-ground influences of mangrove expansion appear to be greatest along low-rainfall coasts where salinities are high and marshes being replaced are carbon poor and dominated by succulent plants. Collectively, these findings complement those from terrestrial ecosystems and reinforce the importance of considering rainfall and plant–soil interactions within predictions of the ecological effects of woody plant encroachment.

Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability.

PubMed

Jiménez, Juan J; Decaëns, Thibaud; Lavelle, Patrick; Rossi, Jean-Pierre

2014-12-05

Studying the drivers and determinants of species, population and community spatial patterns is central to ecology. The observed structure of community assemblages is the result of deterministic abiotic (environmental constraints) and biotic factors (positive and negative species interactions), as well as stochastic colonization events (historical contingency). We analyzed the role of multi-scale spatial component of soil environmental variability in structuring earthworm assemblages in a gallery forest from the Colombian "Llanos". We aimed to disentangle the spatial scales at which species assemblages are structured and determine whether these scales matched those expressed by soil environmental variables. We also tested the hypothesis of the "single tree effect" by exploring the spatial relationships between root-related variables and soil nutrient and physical variables in structuring earthworm assemblages. Multivariate ordination techniques and spatially explicit tools were used, namely cross-correlograms, Principal Coordinates of Neighbor Matrices (PCNM) and variation partitioning analyses. The relationship between the spatial organization of earthworm assemblages and soil environmental parameters revealed explicitly multi-scale responses. The soil environmental variables that explained nested population structures across the multi-spatial scale gradient differed for earthworms and assemblages at the very-fine- (<10 m) to medium-scale (10-20 m). The root traits were correlated with areas of high soil nutrient contents at a depth of 0-5 cm. Information on the scales of PCNM variables was obtained using variogram modeling. Based on the size of the plot, the PCNM variables were arbitrarily allocated to medium (>30 m), fine (10-20 m) and very fine scales (<10 m). Variation partitioning analysis revealed that the soil environmental variability explained from less than 1% to as much as 48% of the observed earthworm spatial variation. A large proportion of the spatial variation did not depend on the soil environmental variability for certain species. This finding could indicate the influence of contagious biotic interactions, stochastic factors, or unmeasured relevant soil environmental variables.

Drivers of spatial heterogeneity in nitrogen processing among three alpine plant communities in the Rocky Mountains

NASA Astrophysics Data System (ADS)

Churchill, A. C.; Beers, A.; Grinath, J.; Bowman, W. D.

2017-12-01

Nitrogen cycling across the globe has been fundamentally altered due to regional elevated N deposition and there is a cascade of ecosystem consequences including shifts in species composition, eutrophication, and soil acidification. Making predictions that encompass the factors that drive these ecosystem changes has frequently been limited to single ecosystem types, or areas with fairly homogenous abiotic conditions. The alpine is an ecosystem type that exhibits changes under relatively low levels of N depositions due to short growing seasons and shallow soils limiting N storage. While recent work provided estimates for the magnitude of N associated with ecosystem changes, less is known about the within-site factors that may interact to stabilize or amplify the differential response of N pools under future conditions of resource deposition. To examine numerous potential within-site and regional factors (both biotic and abiotic) affecting ecosystem N pools we examined the relationship between those factors and a suite of ecosystem pools of N followed by model selection procedures and structural equation modelling. Measurements were conducted at Niwot Ridge Long Term Ecological Research site and in Rocky Mountain National Park in three distinct alpine meadow ecosystems (dry, moist, and wet meadows). These meadows span a moisture gradient as well as plant community composition, thereby providing high variability of potential biotic and abiotic drivers across small spatial scales in the alpine. In general, regional scale abiotic factors such as site levels of annual average N deposition or precipitation were poor predictors of seasonal pools of N, while spring soil water pools of N were negatively correlated with elevation. Models containing multiple abiotic and biotic drivers, however, were best at predicting soil and plant pools of N across the two sites. Future analysis will include highlight interactions among with-site factors affecting N pools in the alpine using structural equation modelling to statistically examine the bidirectional relationship between plant communities and soil pools of N.

Ecosystem development in roadside grasslands: biotic control, plant–soil interactions and dispersal limitations

PubMed Central

García-Palacios, Pablo; Bowker, Matthew A.; Maestre, Fernando T.; Soliveres, Santiago; Valladares, Fernando; Papadopoulos, Jorge; Escudero, Adrián

2015-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant–soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0–2, 7–9 and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts [BSCs], and soil microbial functional diversity [soil microorganisms] affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant–soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: 1) maintain well-conserved natural areas close to roadsides to enhance plant compositional changes towards late-successional stages, 2) increase BSC cover in areas under strong erosion risk, to avoid soil loss, and 3) enhance soil microbial functional diversity in resource-limited areas, to enhance soil C and N accumulation. PMID:22073661

Ecosystem development in roadside grasslands: Biotic control, plant-soil interactions, and dispersal limitations

USGS Publications Warehouse

Garcia-Palacios, P.; Bowker, M.A.; Maestre, F.T.; Soliveres, S.; Valladares, F.; Papadopoulos, J.; Escudero, A.

2011-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant-soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0-2, 7-9, and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts (BSCs), and soil microbial functional diversity (soil microorganisms) affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control, and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant-soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: (1) maintaining wellconserved natural areas close to roadsides to enhance plant compositional changes towards late-successional stages, (2) increasing BSC cover in areas under strong erosion risk, to avoid soil loss, and (3) enhancing soil microbial functional diversity in resource-limited areas, to enhance soil C and N accumulation. ?? 2011 by the Ecological Society of America.

Multiple tuned mass damper based vibration mitigation of offshore wind turbine considering soil-structure interaction

NASA Astrophysics Data System (ADS)

Hussan, Mosaruf; Sharmin, Faria; Kim, Dookie

2017-08-01

The dynamics of jacket supported offshore wind turbine (OWT) in earthquake environment is one of the progressing focuses in the renewable energy field. Soil-structure interaction (SSI) is a fundamental principle to analyze stability and safety of the structure. This study focuses on the performance of the multiple tuned mass damper (MTMD) in minimizing the dynamic responses of the structures objected to seismic loads combined with static wind and wave loads. Response surface methodology (RSM) has been applied to design the MTMD parameters. The analyses have been performed under two different boundary conditions: fixed base (without SSI) and flexible base (with SSI). Two vibration modes of the structure have been suppressed by multi-mode vibration control principle in both cases. The effectiveness of the MTMD in reducing the dynamic response of the structure is presented. The dynamic SSI plays an important role in the seismic behavior of the jacket supported OWT, especially resting on the soft soil deposit. Finally, it shows that excluding the SSI effect could be the reason of overestimating the MTMD performance.

Effects of soil tillage on the microwave emission of soils

NASA Technical Reports Server (NTRS)

Jackson, T. J.; Koopman, G. J.; Oneill, P. E.; Wang, J. R.

1985-01-01

In order to understand the interactions of soil properties and microwave emission better, a series of field experiments were conducted in 1984. Small plots were measured with a truck-mounted passive microwave radiometer operating at 1.4 GHz. These data were collected concurrent with ground observations of soil moisture and bulk density. Treatment effects studied included different soil moisture contents and bulk densities. Evaluations of the data have shown that commonly used models of the dielectric properties of wet soils do not explain the observations obtained in these experiments. This conclusion was based on the fact that the roughness parameters determined through optimization were significantly larger than those observed in similar investigations. These discrepancies are most likely due to the soil structure. Commonly used models assume a homogeneous three phase mixture of soil solids, air and water. Under tilled conditions the soil is actually a two phase mixture of aggregates and voids. Appropriate dielectric models for this tilled condition were evaluated and found to explain the observations. These results indicate that previous conclusions concerning the effects of surface roughness in tilled fields may be incorrect, and they may explain some of the inconsistencies encountered in roughness modeling.

Correlation of soil microbes and soil micro-environment under long-term safflower (Carthamus tinctorius L.) plantation in China.

PubMed

Lu, Shuang; Quan, Wang; Wang, Shao-Ming; Liu, Hong-Ling; Tan, Yong; Zeng, Guang-Ping; Zhang, Xia

2013-04-01

Microbial community structure and ecological functions are influenced by interactions between above and belowground biota. There is an urgent need for intensive monitoring of microbes feedback of soil micro-ecosystem for setting up a good agricultural practice. Recent researches have revealed that many soils characteristic can effect microbial community structure. In the present study factors affecting microbial community structure and soil in Carthamus tinctorius plantations in arid agricultural ecosystem of northern Xinjiang, China were identified. The result of the study revealed that soil type was the key factor in safflower yield; Unscientific field management resulted high fertility level (bacteria dominant) of soil to turn to low fertility level (fungi dominant), and Detruded Canonical Correspondence Analysis (DCCA) showed that soil water content, organic matter, available N, P and K were the dominant factors affecting distribution of microbial community. Soil water content showed a significant positive correlation with soil microbes quantity (P < 0.01), while others showed a significant quantity correlation with soil microbe quantity (P < 0.05).

Evaluating Land-Atmosphere Interactions with the North American Soil Moisture Database

NASA Astrophysics Data System (ADS)

Giles, S. M.; Quiring, S. M.; Ford, T.; Chavez, N.; Galvan, J.

2015-12-01

The North American Soil Moisture Database (NASMD) is a high-quality observational soil moisture database that was developed to study land-atmosphere interactions. It includes over 1,800 monitoring stations the United States, Canada and Mexico. Soil moisture data are collected from multiple sources, quality controlled and integrated into an online database (soilmoisture.tamu.edu). The period of record varies substantially and only a few of these stations have an observation record extending back into the 1990s. Daily soil moisture observations have been quality controlled using the North American Soil Moisture Database QAQC algorithm. The database is designed to facilitate observationally-driven investigations of land-atmosphere interactions, validation of the accuracy of soil moisture simulations in global land surface models, satellite calibration/validation for SMOS and SMAP, and an improved understanding of how soil moisture influences climate on seasonal to interannual timescales. This paper provides some examples of how the NASMD has been utilized to enhance understanding of land-atmosphere interactions in the U.S. Great Plains.

Interactions in Natural Colloid Systems "Biosolids" - Soil and Plant

NASA Astrophysics Data System (ADS)

Kalinichenko, Kira V.; Nikovskaya, Galina N.; Ulberg, Zoya R.

2016-04-01

The "biosolids" are complex biocolloid system arising in huge amounts (mln tons per year) from biological municipal wastewater treatment. These contain clusters of nanoparticles of heavy metal compounds (in slightly soluble or unsoluble forms, such as phosphates, sulphates, carbonates, hydroxides, and etc.), cells, humic substances and so on, involved in exopolysaccharides (EPS) net matrix. One may consider that biosolids are the natural nanocomposite. Due to the presence of nitrogen, phosphorus, potassium and other macro- and microelements (heavy metals), vitamins, aminoacids, etc., the biosolids are a depot of bioelements for plant nutrition. Thus, it is generally recognized that most rationally to utilize them for land application. For this purpose the biocolloid process was developed in biosolids system by initiation of microbial vital ability followed by the synthesis of EPS, propagation of ecologically important microorganisms, loosening of the structure and weakening of the coagulation contacts between biosolids colloids, but the structure integrity maintaining [1,2]. It was demonstrated that the applying of biosolids with metabolizing microorganisms to soil provided the improving soil structure, namely the increasing of waterstable aggregates content (70% vs. 20%). It occurs due to flocculation ability of biosolids EPS. The experimental modelling of mutual interactions in systems of soils - biosolids (with metabolizing microorganisms) were realized and their colloid and chemical mechanisms were formulated [3]. As it is known, the most harmonious plant growth comes at a prolonged entering of nutrients under the action of plant roots exudates which include pool of organic acids and polysaccharides [4]. Special investigations showed that under the influence of exudates excreted by growing plants, the biosolids microelements can release gradually from immobilized state into environment and are able to absorb by plants. Thus, the biosolids can serve as an active component of soil substrate. Soil enrichment with biosolids nanocomposite resulted in an improving of its structures, a faster growth of plants and substantial harvest increase, as compared with control (unfertilized) soil. 1. Kalinichenko KV, Nikovskaya GN, and Ulberg ZR (2012) Bioextraction of heavy metals from colloidal sludge systems. Colloid Journ. 74(5): 553-557. 2. Kalinichenko KV, Nikovskaya GN, and Ulberg ZR (2013) Changes in the surface properties and stability of biocolloids of a sludge system upon extraction of heavy metals. Colloid Journ. 75(3): 274-278. 3. Nikovskaya GN, et al (2006) The influence of different reclamation agents and microorganisms on the aggregative stability of the colloidal fraction of meadow chernozem soil. Colloid Journal. 68 (3): 345-349. 4. Dakora FD, Phillips DA (2002) Root exudates as mediators of mineral acquisition in low-nutrient environments. Plant and Soil. 1: 35-47.

Divergent evapotranspiration partition dynamics between shrubs and grasses in a shrub-encroached steppe ecosystem.

PubMed

Wang, Pei; Li, Xiao-Yan; Wang, Lixin; Wu, Xiuchen; Hu, Xia; Fan, Ying; Tong, Yaqin

2018-06-04

Previous evapotranspiration (ET) partitioning studies have usually neglected competitions and interactions between antagonistic plant functional types. This study investigated whether shrubs and grasses have divergent ET partition dynamics impacted by different water-use patterns, canopy structures, and physiological properties in a shrub-encroached steppe ecosystem in Inner Mongolia, China. The soil water-use patterns of shrubs and grasses have been quantified by an isotopic tracing approach and coupled into an improved multisource energy balance model to partition ET fluxes into soil evaporation, grass transpiration, and shrub transpiration. The mean fractional contributions to total ET were 24 ± 13%, 20 ± 4%, and 56 ± 16% for shrub transpiration, grass transpiration, and soil evaporation respectively during the growing season. Difference in ecohydrological connectivity and leaf development both contributed to divergent transpiration partitioning between shrubs and grasses. Shrub-encroachment processes result in larger changes in the ET components than in total ET flux, which could be well explained by changes in canopy resistance, an ecosystem function dominated by the interaction of soil water-use patterns and ecosystem structure. The analyses presented here highlight the crucial effects of vegetation structural changes on the processes of land-atmosphere interaction and climate feedback. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China.

PubMed

Yao, Xiaodong; Zhang, Naili; Zeng, Hui; Wang, Wei

2018-07-15

Although the patterns and drivers of soil microbial community composition are well studied, little is known about the effects of plant-soil interactions and soil depth on soil microbial distribution at a regional scale. We examined 195 soil samples from 13 sites along a climatic transect in the temperate grasslands of northern China to measure the composition of and factors influencing soil microbial communities within a 1-m soil profile. Soil microbial community composition was measured using phospholipid fatty acids (PLFA) analysis. Fungi predominated in topsoil (0-10 cm) and bacteria and actinomycetes in deep soils (40-100 cm), independent of steppe types. This variation was explained by contemporary environmental factors (including above- and below-ground plant biomass, soil physicochemical and climatic factors) >58% in the 0-40 cm of soil depth, but <45% in deep soils. Interestingly, when we considered the interactive effects between plant traits (above ground biomass and root biomass) and soil factors (pH, clay content, and soil total carbon, nitrogen, phosphorous), we observed a significant interaction effect occurring at depths of 10-20 cm soil layer, due to different internal and external factors of the plant-soil system along the soil profile. These results improve understanding of the drivers of soil microbial community composition at regional scales. Copyright © 2018 Elsevier B.V. All rights reserved.

Topsoil structure stability in a restored floodplain: Impacts of fluctuating water levels, soil parameters and ecosystem engineers.

PubMed

Schomburg, A; Schilling, O S; Guenat, C; Schirmer, M; Le Bayon, R C; Brunner, P

2018-10-15

Ecosystem services provided by floodplains are strongly controlled by the structural stability of soils. The development of a stable structure in floodplain soils is affected by a complex and poorly understood interplay of hydrological, physico-chemical and biological processes. This paper aims at analysing relations between fluctuating groundwater levels, soil physico-chemical and biological parameters on soil structure stability in a restored floodplain. Water level fluctuations in the soil are modelled using a numerical surface-water-groundwater flow model and correlated to soil physico-chemical parameters and abundances of plants and earthworms. Causal relations and multiple interactions between the investigated parameters are tested through structural equation modelling (SEM). Fluctuating water levels in the soil did not directly affect the topsoil structure stability, but indirectly through affecting plant roots and soil parameters that in turn determine topsoil structure stability. These relations remain significant for mean annual days of complete and partial (>25%) water saturation. Ecosystem functioning of a restored floodplain might already be affected by the fluctuation of groundwater levels alone, and not only through complete flooding by surface water during a flood period. Surprisingly, abundances of earthworms did not show any relation to other variables in the SEM. These findings emphasise that earthworms have efficiently adapted to periodic stress and harsh environmental conditions. Variability of the topsoil structure stability is thus stronger driven by the influence of fluctuating water levels on plants than by the abundance of earthworms. This knowledge about the functional network of soil engineering organisms, soil parameters and fluctuating water levels and how they affect soil structural stability is of fundamental importance to define management strategies of near-natural or restored floodplains in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

Wet-dry cycles impact DOM retention in subsurface soils

NASA Astrophysics Data System (ADS)

Olshansky, Yaniv; Root, Robert A.; Chorover, Jon

2018-02-01

Transport and reactivity of carbon in the critical zone are highly controlled by reactions of dissolved organic matter (DOM) with subsurface soils, including adsorption, transformation and exchange. These reactions are dependent on frequent wet-dry cycles common to the unsaturated zone, particularly in semi-arid regions. To test for an effect of wet-dry cycles on DOM interaction and stabilization in subsoils, samples were collected from subsurface (Bw) horizons of an Entisol and an Alfisol from the Catalina-Jemez Critical Zone Observatory and sequentially reacted (four batch steps) with DOM extracted from the corresponding soil litter layers. Between each reaction step, soils either were allowed to air dry (wet-dry treatment) before introduction of the following DOM solution or were maintained under constant wetness (continually wet treatment). Microbial degradation was the dominant mechanism of DOM loss from solution for the Entisol subsoil, which had higher initial organic C content, whereas sorptive retention predominated in the lower C Alfisol subsoil. For a given soil, bulk dissolved organic C losses from solution were similar across treatments. However, a combination of Fourier transform infrared (FTIR) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopic analyses revealed that wet-dry treatments enhanced the interactions between carboxyl functional groups and soil particle surfaces. Scanning transmission X-ray microscopy (STXM) data suggested that cation bridging by Ca2+ was the primary mechanism for carboxyl association with soil surfaces. STXM data also showed that spatial fractionation of adsorbed OM on soil organo-mineral surfaces was diminished relative to what might be inferred from previously published observations pertaining to DOM fractionation on reaction with specimen mineral phases. This study provides direct evidence of the role of wet-dry cycles in affecting sorption reactions of DOM to a complex soil matrix. In the soil environment, where wet-dry cycles occur at different frequencies from site to site and along the soil profile, different interactions between DOM and soil surfaces are expected and need to be considered for the overall assessment of carbon dynamics.

Basin-wide variations in Amazon forest structure and function are mediated by both soils and climate

NASA Astrophysics Data System (ADS)

Quesada, C. A.; Phillips, O. L.; Schwarz, M.; Czimczik, C. I.; Baker, T. R.; Patiño, S.; Fyllas, N. M.; Hodnett, M. G.; Herrera, R.; Almeida, S.; Alvarez Dávila, E.; Arneth, A.; Arroyo, L.; Chao, K. J.; Dezzeo, N.; Erwin, T.; di Fiore, A.; Higuchi, N.; Honorio Coronado, E.; Jimenez, E. M.; Killeen, T.; Lezama, A. T.; Lloyd, G.; López-González, G.; Luizão, F. J.; Malhi, Y.; Monteagudo, A.; Neill, D. A.; Núñez Vargas, P.; Paiva, R.; Peacock, J.; Peñuela, M. C.; Peña Cruz, A.; Pitman, N.; Priante Filho, N.; Prieto, A.; Ramírez, H.; Rudas, A.; Salomão, R.; Santos, A. J. B.; Schmerler, J.; Silva, N.; Silveira, M.; Vásquez, R.; Vieira, I.; Terborgh, J.; Lloyd, J.

2012-06-01

Forest structure and dynamics vary across the Amazon Basin in an east-west gradient coincident with variations in soil fertility and geology. This has resulted in the hypothesis that soil fertility may play an important role in explaining Basin-wide variations in forest biomass, growth and stem turnover rates. Soil samples were collected in a total of 59 different forest plots across the Amazon Basin and analysed for exchangeable cations, carbon, nitrogen and pH, with several phosphorus fractions of likely different plant availability also quantified. Physical properties were additionally examined and an index of soil physical quality developed. Bivariate relationships of soil and climatic properties with above-ground wood productivity, stand-level tree turnover rates, above-ground wood biomass and wood density were first examined with multivariate regression models then applied. Both forms of analysis were undertaken with and without considerations regarding the underlying spatial structure of the dataset. Despite the presence of autocorrelated spatial structures complicating many analyses, forest structure and dynamics were found to be strongly and quantitatively related to edaphic as well as climatic conditions. Basin-wide differences in stand-level turnover rates are mostly influenced by soil physical properties with variations in rates of coarse wood production mostly related to soil phosphorus status. Total soil P was a better predictor of wood production rates than any of the fractionated organic- or inorganic-P pools. This suggests that it is not only the immediately available P forms, but probably the entire soil phosphorus pool that is interacting with forest growth on longer timescales. A role for soil potassium in modulating Amazon forest dynamics through its effects on stand-level wood density was also detected. Taking this into account, otherwise enigmatic variations in stand-level biomass across the Basin were then accounted for through the interacting effects of soil physical and chemical properties with climate. A hypothesis of self-maintaining forest dynamic feedback mechanisms initiated by edaphic conditions is proposed. It is further suggested that this is a major factor determining endogenous disturbance levels, species composition, and forest productivity across the Amazon Basin.

Distinct respiratory responses of soils to complex organic substrate are governed predominantly by soil architecture and its microbial community.

PubMed

Fraser, F C; Todman, L C; Corstanje, R; Deeks, L K; Harris, J A; Pawlett, M; Whitmore, A P; Ritz, K

2016-12-01

Factors governing the turnover of organic matter (OM) added to soils, including substrate quality, climate, environment and biology, are well known, but their relative importance has been difficult to ascertain due to the interconnected nature of the soil system. This has made their inclusion in mechanistic models of OM turnover or nutrient cycling difficult despite the potential power of these models to unravel complex interactions. Using high temporal-resolution respirometery (6 min measurement intervals), we monitored the respiratory response of 67 soils sampled from across England and Wales over a 5 day period following the addition of a complex organic substrate (green barley powder). Four respiratory response archetypes were observed, characterised by different rates of respiration as well as different time-dependent patterns. We also found that it was possible to predict, with 95% accuracy, which type of respiratory behaviour a soil would exhibit based on certain physical and chemical soil properties combined with the size and phenotypic structure of the microbial community. Bulk density, microbial biomass carbon, water holding capacity and microbial community phenotype were identified as the four most important factors in predicting the soils' respiratory responses using a Bayesian belief network. These results show that the size and constitution of the microbial community are as important as physico-chemical properties of a soil in governing the respiratory response to OM addition. Such a combination suggests that the 'architecture' of the soil, i.e. the integration of the spatial organisation of the environment and the interactions between the communities living and functioning within the pore networks, is fundamentally important in regulating such processes.

Seismic Response of Steel Braced Building Frame Considering Soil Structure Interaction (SSI): An Experimental Study

NASA Astrophysics Data System (ADS)

Hirave, Vivek; Kalyanshetti, Mahesh

2018-02-01

Conventional fixed-base analysis ignoring the effect of soil-flexibility may result in unsafe design. Therefore, to evaluate the realistic behavior of structure the soil structure interaction (SSI) effect shall be incorporated in the analysis. In seismic analysis, provision of bracing system is one of the important option for the structure to have sufficient strength with adequate stiffness to resist lateral forces. The different configuration of these bracing systems alters the response of buildings, and therefore, it is important to evaluate the most effective bracing systems in view point of stability against SSI effect. In present study, three RC building frames, G+3, G+5 and G+7 and their respective scaled down steel model with two types of steel bracing system incorporating the effect of soil flexibility is considered for experimental and analytical study. The analytical study is carried out using Elastic continuum approach and the experimental study is carried out using Shake Table. The influence of SSI on various seismic parameters is presented. The study reveals that, steel bracing system is beneficial to control SSI effect and it is observed that V bracing is more effective, in resisting seismic load considering SSI.

Exploring plant root traits and fungal interactions governing plant community structure: Re-focusing long standing questions.

USDA-ARS?s Scientific Manuscript database

Resource availability has long been recognized for playing a major role in structuring plant communities. Nonetheless, a functional understanding of root traits and interactions with soil organisms involved in acquiring those resources has largely remained out of focus and outside mainstream ecolog...

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Arbuscule mycorrhizae: A linkage between erosion and plant processes in a southwest grassland

Treesearch

Mary O' Dea; D. Phillip Guertin; C. P. P. Reid

2000-01-01

Plant and soil processes within a natural ecosystem interact with surface hydrology through their influence on surface roughness, soil structure, and evaporation, and through their relation with soil biota. In the Southwest, decreases in perennial grass cover and erosion on uplands and stream channels can initiate a decline in watershed condition. Agronomic literature...

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE PAGES

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae; ...

2017-03-22

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

USGS Publications Warehouse

Chung, Y. Anny; Sinsabaugh, Robert L; Kuske, Cheryl R.; Reed, Sasha C.; Rudgers, Jennifer A.

2017-01-01

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefits of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. The findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.

Improving design phase evaluations for high pile rebound sites [summary].

DOT National Transportation Integrated Search

2016-05-01

In Florida, many structures are built on driven piles. Though it seems straightforward, pile : driving involves complex interactions between the pile, the hammer, the soil, and driving : procedures. Soils can even rebound, or push back, after each ha...

Interactive effects of elevated ozone and UV-B radiation on soil nematode diversity.

PubMed

Bao, Xuelian; Li, Qi; Hua, Jianfeng; Zhao, Tianhong; Liang, Wenju

2014-01-01

Ultraviolet-B (UV-B) radiation and elevated tropospheric ozone may cause reductions in the productivity and quality of important agricultural crops. However, research regarding their interactive effect is still scarce, especially on the belowground processes. Using the open top chambers experimental setup, we monitored the response of soil nematodes to the elevated O3 and UV-B radiation individually as well as in combination. Our results indicated that elevated O3 and UV-B radiation have impact not only on the belowground biomass of plants, but also on the community structure and functional diversity of soil nematodes. The canonical correspondence analysis suggested that soil pH, shoot biomass and microbial biomass C and N were relevant parameters that influencing soil nematode distribution. The interactive effects of elevated O3 and UV-B radiation was only observed on the abundance of bacterivores. UV-B radiation significantly increased the abundance of total nematodes and bacterivores in comparison with the control at pod-filling stage of soybean. Following elevated O3, nematode diversity index decreased and dominance index increased relative to the control at pod-filling stage of soybean. Nematode functional diversity showed response to the effects of elevated O3 and UV-B radiation at pod-bearing stage. Higher enrichment index and lower structure index in the treatment with both elevated O3 and UV-B radiation indicated a stressed soil condition and degraded soil food web. However, the ratios of nematode trophic groups suggested that the negative effects of elevated O3 on soil food web may be weakened by the UV-B radiations.

Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence.

PubMed

Lekberg, Ylva; Bever, James D; Bunn, Rebecca A; Callaway, Ragan M; Hart, Miranda M; Kivlin, Stephanie N; Klironomos, John; Larkin, Beau G; Maron, John L; Reinhart, Kurt O; Remke, Michael; van der Putten, Wim H

2018-06-12

Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition vs. plant-soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter- to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbour identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low-resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure. © 2018 John Wiley & Sons Ltd/CNRS.

Impact of elevated precipitation, nitrogen deposition and warming on soil respiration in a temperate desert

NASA Astrophysics Data System (ADS)

Yue, Ping; Cui, Xiaoqing; Gong, Yanming; Li, Kaihui; Goulding, Keith; Liu, Xuejun

2018-04-01

Soil respiration (Rs) is the most important source of carbon dioxide emissions from soil to atmosphere. However, it is unclear what the interactive response of Rs would be to environmental changes such as elevated precipitation, nitrogen (N) deposition and warming, especially in unique temperate desert ecosystems. To investigate this an in situ field experiment was conducted in the Gurbantunggut Desert, northwest China, from September 2014 to October 2016. The results showed that precipitation and N deposition significantly increased Rs, but warming decreased Rs, except in extreme precipitation events, which was mainly through its impact on the variation of soil moisture at 5 cm depth. In addition, the interactive response of Rs to combinations of the factors was much less than that of any single-factor, and the main response was a positive effect, except for the response from the interaction of increased precipitation and high N deposition (60 kg N ha-1 yr-1). Although Rs was found to show a unimodal change pattern with the variation of soil moisture, soil temperature and soil NH4+-N content, and it was significantly positively correlated to soil dissolved organic carbon (DOC) and pH, a structural equation model found that soil temperature was the most important controlling factor. Those results indicated that Rs was mainly interactively controlled by the soil multi-environmental factors and soil nutrients, and was very sensitive to elevated precipitation, N deposition and warming. However, the interactions of multiple factors largely reduced between-year variation of Rs more than any single-factor, suggesting that the carbon cycle in temperate deserts could be profoundly influenced by positive carbon-climate feedback.

Reconstruction of food webs in biological soil crusts using metabolomics.

NASA Astrophysics Data System (ADS)

Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; Nunes Da Rocha, Ulisses; Bowen, Benjamin P.; Karaoz, Ulas; Cadillo-Quiroz, Hinsby; Garcia-Pichel, Ferran; Northen, Trent R.

2015-04-01

Biological soil crusts (BSCs) are communities of organisms inhabiting the upper layer of soil in arid environments. BSCs persist in a dessicated dormant state for extended periods of time and experience pulsed periods of activity facilitated by infrequent rainfall. Microcoleus vaginatus, a non-diazotrophic filamentous cyanobacterium, is the key primary producer in BSCs in the Colorado Plateau and is an early pioneer in colonizing arid environments. Over decades, BSCs proceed through developmental stages with increasing complexity of constituent microorganisms and macroscopic properties. Metabolic interactions among BSC microorganisms probably play a key role in determining the community dynamics and cycling of carbon and nitrogen. However, these metabolic interactions have not been studied systematically. Towards this goal, exometabolomic analysis was performed using liquid chromatography coupled to tandem mass spectrometry on biological soil crust pore water and spent media of key soil bacterial isolates. Comparison of spent vs. fresh media was used to determine uptake or release of metabolites by specific microbes. To link pore water experiments with isolate studies, metabolite extracts of authentic soil were used as supplements for isolate exometabolomic profiling. Our soil metabolomics methods detected hundreds of metabolites from soils including many novel compounds. Overall, Microcoleus vaginatus was found to release and utilize a broad range of metabolites. Many of these metabolites were also taken up by heterotrophs but there were surprisingly few metabolites uptaken by all isolates. This points to a competition for a small set of central metabolites and specialization of individual heterotrophs towards a diverse pool of available organic nutrients. Overall, these data suggest that understanding the substrate specialization of biological soil crust bacteria can help link community structure to nutrient cycling.

Denitrification in Agricultural Soils: Integrated control and Modelling at various scales (DASIM)

NASA Astrophysics Data System (ADS)

Müller, Christoph; Well, Reinhard; Böttcher, Jürgen; Butterbach-Bahl, Klaus; Dannenmann, Michael; Deppe, Marianna; Dittert, Klaus; Dörsch, Peter; Horn, Marcus; Ippisch, Olaf; Mikutta, Robert; Senbayram, Mehmet; Vogel, Hans-Jörg; Wrage-Mönnig, Nicole; Müller, Carsten

2016-04-01

The new research unit DASIM brings together the expertise of 11 working groups to study the process of denitrification at unprecedented spatial and temporal resolution. Based on state-of-the art analytical techniques our aim is to develop improved denitrification models ranging from the microscale to the field/plot scale. Denitrification, the process of nitrate reduction allowing microbes to sustain respiration under anaerobic conditions, is the key process returning reactive nitrogen as N2to the atmosphere. Actively denitrifying communities in soil show distinct regulatory phenotypes (DRP) with characteristic controls on the single reaction steps and end-products. It is unresolved whether DRPs are anchored in the taxonomic composition of denitrifier communities and how environmental conditions shape them. Despite being intensively studied for more than 100 years, denitrification rates and emissions of its gaseous products can still not be satisfactorily predicted. While the impact of single environmental parameters is well understood, the complexity of the process itself with its intricate cellular regulation in response to highly variable factors in the soil matrix prevents robust prediction of gaseous emissions. Key parameters in soil are pO2, organic matter content and quality, pH and the microbial community structure, which in turn are affected by the soil structure, chemistry and soil-plant interactions. In the DASIM research unit, we aim at the quantitative prediction of denitrification rates as a function of microscale soil structure, organic matter quality, DRPs and atmospheric boundary conditions via a combination of state-of-the-art experimental and analytical tools (X-ray μCT, 15N tracing, NanoSIMS, microsensors, advanced flux detection, NMR spectroscopy, and molecular methods including next generation sequencing of functional gene transcripts). We actively seek collaboration with researchers working in the field of denitrification.

Evaluation of dynamic response for monopole and hybrid wind mill tower

NASA Astrophysics Data System (ADS)

Shah, Hemal J.; Desai, Atul K.

2017-07-01

The wind mill towers are constructed using monopoles or lattice type tower. As the height of tower increases it gives more power but it becomes uneconomical, so in the present research work innovative wind mill tower such as combination of monopole and lattice tower is analyzed using FEM software. When the tall structures are constructed on soft soil it becomes dynamically sensitive so 3 types of soil such as hard, medium and soft soil is also modeled and the innovative tower is studied for different operating frequencies of wind turbine. From study it is concluded that the innovative tower will reduce resonance condition considering soil structure interaction.

Experimental sensitivity analysis of subsoil-slab behaviour regarding degree of fibre-concrete slab reinforcement

NASA Astrophysics Data System (ADS)

Hrubesova, E.; Lahuta, H.; Mohyla, M.; Quang, T. B.; Phi, N. D.

2018-04-01

The paper is focused on the sensitivity analysis of behaviour of the subsoil – foundation system as regards the variant properties of fibre-concrete slab resulting into different relative stiffness of the whole cooperating system. The character of slab and its properties are very important for the character of external load transfer, but the character of subsoil cannot be neglected either because it determines the stress-strain behaviour of the all system and consequently the bearing capacity of structure. The sensitivity analysis was carried out based on experimental results, which include both the stress values in soil below the foundation structure and settlements of structure, characterized by different quantity of fibres in it. Flat dynamometers GEOKON were used for the stress measurements below the observed slab, the strains inside slab were registered by tensometers, the settlements were monitored geodetically. The paper is focused on the comparison of soil stresses below the slab for different quantity of fibres in structure. The results obtained from the experimental stand can contribute to more objective knowledge of soil – slab interaction, to the evaluation of real carrying capacity of the slab, to the calibration of corresponding numerical models, to the optimization of quantity of fibres in the slab, and finally, to higher safety and more economical design of slab.

Using operational and defined fractions to assess soil organic matter stabilization and structure

NASA Astrophysics Data System (ADS)

Horwath, W. R.

2015-12-01

Studies on soil organic matter (SOM) began with alkaline solvents revealing a dark colored substance that could be isolated under low pH. Further studies revealed fulvic and humic acids and humin fractions leading to theories on functional groups and metal-clay bridging mechanisms. The fate of isotopes in these fractions revealed soil carbon pools with varying turnover rates with half the soil carbon (C) in humin and acid hydrolyzed fractions over 1000 years old. These results are the basis of the three pool conceptual framework used in many biogeochemical models. Theories on the role of functional groups and compound classes further elaborated concepts on physical (aggregates) and chemical mechanisms of C stabilization. With the advance of analytical instrumentation, the operational fractions were further defined to the compound and molecular levels. These studies confirmed the majority of soil C is microbially derived. Our observation that all microbial groups contributed nonselectively to soil C maintenance independent of mineralogy suggests that compound characteristics within integrated structures are more important than the source of individual compounds for stabilizing soil C. In dissolved organic C floccing studies using Near Edge X-ray Fine Structure analysis, we found that aromatic compounds interacted first with Fe, however, the majority of direct bonds to Fe were polysaccharides, reinforcing that an integrative chemical structure rather than direct bonds imparted stability in organo-metal interactions. Using a novel differential scanning calorimeter coupled to an isotope ratio mass spectrometer setup, we confirmed that the presence of clays (independent of clay type) increased the microbial utilization of calcium stabilized high versus low temperature compounds, asserting that higher temperature compounds (i.e., phenolics) are likely less tightly bound by clay minerals. The integration of operational and defined fractions of SOM remains a legitimate approach to examine SOM structure and stabilization across scales of soil development and management.

Sorption interactions of organic compounds with soils affected by agricultural olive mill wastewater.

PubMed

Keren, Yonatan; Borisover, Mikhail; Bukhanovsky, Nadezhda

2015-11-01

The organic compound-soil interactions may be strongly influenced by changes in soil organic matter (OM) which affects the environmental fate of multiple organic pollutants. The soil OM changes may be caused by land disposal of various OM-containing wastes. One unique type of OM-rich waste is olive mill-related wastewater (OMW) characterized by high levels of OM, the presence of fatty aliphatics and polyphenolic aromatics. The systematic data on effects of the land-applied OMW on organic compound-soil interactions is lacking. Therefore, aqueous sorption of simazine and diuron, two herbicides, was examined in batch experiments onto three soils, including untreated and OMW-affected samples. Typically, the organic compound-soil interactions increased following the prior land application of OMW. This increase is associated with the changes in sorption mechanisms and cannot be attributed solely to the increase in soil organic carbon content. A novel observation is that the OMW application changes the soil-sorbent matrix in such a way that the solute uptake may become cooperative or the existing ability of a soil sorbent to cooperatively sorb organic molecules from water may become characterized by a larger affinity. The remarkable finding of this study was that in some cases a cooperative uptake of organic molecules by soils makes itself evident in distinct sigmoidal sorption isotherms rarely observed in soil sorption of non-ionized organic compounds; the cooperative herbicide-soil interactions may be characterized by the Hill model coefficients. However, no single trend was found for the effect of applied OMW on the mechanisms of organic compound-soil interactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluation of soil-foundation-structure interaction effects on seismic response demands of multi-story MRF buildings on raft foundations

NASA Astrophysics Data System (ADS)

Abdel Raheem, Shehata E.; Ahmed, Mohamed M.; Alazrak, Tarek M. A.

2015-03-01

Soil conditions have a great deal to do with damage to structures during earthquakes. Hence the investigation on the energy transfer mechanism from soils to buildings during earthquakes is critical for the seismic design of multi-story buildings and for upgrading existing structures. Thus, the need for research into soil-structure interaction (SSI) problems is greater than ever. Moreover, recent studies show that the effects of SSI may be detrimental to the seismic response of structure and neglecting SSI in analysis may lead to un-conservative design. Despite this, the conventional design procedure usually involves assumption of fixity at the base of foundation neglecting the flexibility of the foundation, the compressibility of the underneath soil and, consequently, the effect of foundation settlement on further redistribution of bending moment and shear force demands. Hence the SSI analysis of multi-story buildings is the main focus of this research; the effects of SSI are analyzed for typical multi-story building resting on raft foundation. Three methods of analysis are used for seismic demands evaluation of the target moment-resistant frame buildings: equivalent static load; response spectrum methods and nonlinear time history analysis with suit of nine time history records. Three-dimensional FE model is constructed to investigate the effects of different soil conditions and number of stories on the vibration characteristics and seismic response demands of building structures. Numerical results obtained using SSI model with different soil conditions are compared to those corresponding to fixed-base support modeling assumption. The peak responses of story shear, story moment, story displacement, story drift, moments at beam ends, as well as force of inner columns are analyzed. The results of different analysis approaches are used to evaluate the advantages, limitations, and ease of application of each approach for seismic analysis.

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem.

PubMed

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan; Liu, Qing

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai-Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems.

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem

PubMed Central

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai–Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems. PMID:29668711

Invasive soil organisms and their effects on belowground processes

Treesearch

Erik Lilleskov; Jr. Mac A. Callaham; Richard Pouyat; Jane E. Smith; Michael Castellano; Grizelle Gonzalez; D. Jean Lodge; Rachel Arango; Frederick Green

2010-01-01

Invasive species have a wide range of effects on soils and their inhabitants. By altering soils, through their direct effects on native soil organisms (including plants), and by their interaction with the aboveground environment, invasive soil organisms can have dramatic effects on the environment, the economy and human health. The most widely recognized effects...

Plant roots: understanding structure and function in an ocean of complexity

PubMed Central

Ryan, Peter R.; Delhaize, Emmanuel; Watt, Michelle; Richardson, Alan E.

2016-01-01

Background The structure and function of plant roots and their interactions with soil are exciting scientific frontiers that will ultimately reveal much about our natural systems, global water and mineral and carbon cycles, and help secure food supplies into the future. This Special Issue presents a collection of papers that address topics at the forefront of our understanding of root biology. Scope These papers investigate how roots cope with drought, nutrient deficiencies, toxicities and soil compaction as well as the interactions that roots have with soil microorganisms. Roots of model plant species, annual crops and perennial species are studied in short-term experiments through to multi-year trials. Spatial scales range from the gene up to farming systems and nutrient cycling. The diverse, integrated approaches described by these studies encompass root genetics as applied to soil management, as well as documenting the signalling processes occurring between roots and shoots and between roots and soil. Conclusions This Special Issue on roots presents invited reviews and research papers covering a span of topics ranging from fundamental aspects of anatomy, growth and water uptake to roots in crop and pasture systems. Understanding root structure and function and adaptation to the abiotic and biotic stresses encountered in field conditions is important for sustainable agricultural production and better management of natural systems.

13C AND 15N IN MICROARTHROPODS REVEAL LITTLE RESPONSE OF DOUGLAS-FIR ECOSYSTEMS TO CLIMATE CHANGE

EPA Science Inventory

Understanding ecosystem carbon (C) and nitrogen (N) cycling under global change requires experiments maintaining natural interactions among soil structure, soil communities, nutrient availability, and plant growth. In model Douglas-fir ecosystems maintained for five growing seaso...

Co-simulation coupling spectral/finite elements for 3D soil/structure interaction problems

NASA Astrophysics Data System (ADS)

Zuchowski, Loïc; Brun, Michael; De Martin, Florent

2018-05-01

The coupling between an implicit finite elements (FE) code and an explicit spectral elements (SE) code has been explored for solving the elastic wave propagation in the case of soil/structure interaction problem. The coupling approach is based on domain decomposition methods in transient dynamics. The spatial coupling at the interface is managed by a standard coupling mortar approach, whereas the time integration is dealt with an hybrid asynchronous time integrator. An external coupling software, handling the interface problem, has been set up in order to couple the FE software Code_Aster with the SE software EFISPEC3D.

Hydrologic dynamics and ecosystem structure.

PubMed

Rodríguez-Iturbe, I

2003-01-01

Ecohydrology is the science that studies the mutual interaction between the hydrological cycle and ecosystems. Such an interaction is especially intense in water-controlled ecosystems, where water may be a limiting factor, not only because of its scarcity, but also because of its intermittent and unpredictable appearance. Hydrologic dynamics is shown to be a crucial factor for ecological patterns and processes. The probabilistic structure of soil moisture in time and space is presented as the key linkage between soil, climate and vegetation dynamics. Nutrient cycles, vegetation coexistence and plant response to environmental conditions are all intimately linked to the stochastic fluctuation of the hydrologic inputs driving an ecosystem.

Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils.

PubMed

Rashid, Muhammad Imtiaz; Mujawar, Liyakat Hamid; Shahzad, Tanvir; Almeelbi, Talal; Ismail, Iqbal M I; Oves, Mohammad

2016-02-01

Intensive agricultural practices and cultivation of exhaustive crops has deteriorated soil fertility and its quality in agroecosystems. According to an estimate, such practices will convert 30% of the total world cultivated soil into degraded land by 2020. Soil structure and fertility loss are one of the main causes of soil degradation. They are also considered as a major threat to crop production and food security for future generations. Implementing safe and environmental friendly technology would be viable solution for achieving sustainable restoration of degraded soils. Bacterial and fungal inocula have a potential to reinstate the fertility of degraded land through various processes. These microorganisms increase the nutrient bioavailability through nitrogen fixation and mobilization of key nutrients (phosphorus, potassium and iron) to the crop plants while remediate soil structure by improving its aggregation and stability. Success rate of such inocula under field conditions depends on their antagonistic or synergistic interaction with indigenous microbes or their inoculation with organic fertilizers. Co-inoculation of bacteria and fungi with or without organic fertilizer are more beneficial for reinstating the soil fertility and organic matter content than single inoculum. Such factors are of great importance when considering bacteria and fungi inocula for restoration of degraded soils. The overview of presented mechanisms and interactions will help agriculturists in planning sustainable management strategy for reinstating the fertility of degraded soil and assist them in reducing the negative impact of artificial fertilizers on our environment. Copyright © 2015 Elsevier GmbH. All rights reserved.

A radiosity-based model to compute the radiation transfer of soil surface

NASA Astrophysics Data System (ADS)

Zhao, Feng; Li, Yuguang

2011-11-01

A good understanding of interactions of electromagnetic radiation with soil surface is important for a further improvement of remote sensing methods. In this paper, a radiosity-based analytical model for soil Directional Reflectance Factor's (DRF) distributions was developed and evaluated. The model was specifically dedicated to the study of radiation transfer for the soil surface under tillage practices. The soil was abstracted as two dimensional U-shaped or V-shaped geometric structures with periodic macroscopic variations. The roughness of the simulated surfaces was expressed as a ratio of the height to the width for the U and V-shaped structures. The assumption was made that the shadowing of soil surface, simulated by U or V-shaped grooves, has a greater influence on the soil reflectance distribution than the scattering properties of basic soil particles of silt and clay. Another assumption was that the soil is a perfectly diffuse reflector at a microscopic level, which is a prerequisite for the application of the radiosity method. This radiosity-based analytical model was evaluated by a forward Monte Carlo ray-tracing model under the same structural scenes and identical spectral parameters. The statistics of these two models' BRF fitting results for several soil structures under the same conditions showed the good agreements. By using the model, the physical mechanism of the soil bidirectional reflectance pattern was revealed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suresh, Niraj; Stephens, Sean A.; Adams, Lexor

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and forest management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving the plant. X ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. Our group at the Environmental Molecular Sciences Laboratory (EMSL) has developed an XCT-based tool to image and quantitatively analyze plant root structures in their native soil environment. XCT data collected on amore » Prairie dropseed (Sporobolus heterolepis) specimen was used to visualize its root structure. A combination of open-source software RooTrak and DDV were employed to segment the root from the soil, and calculate its isosurface, respectively. Our own computer script named 3DRoot-SV was developed and used to calculate root volume and surface area from a triangular mesh. The process utilizing a unique combination of tools, from imaging to quantitative root analysis, including the 3DRoot-SV computer script, is described.« less

MSATT Workshop on Innovative Instrumentation for the In Situ Study of Atmosphere-Surface Interactions on Mars

NASA Technical Reports Server (NTRS)

Fegley, Bruce, Jr. (Editor); Waenke, Heinrich (Editor)

1992-01-01

Papers accepted for the Mars Surface and Atmosphere Through Time (MSATT) Workshop on Innovative Instruments for the In Situ Study of Atmosphere-Surface Interaction of Mars, 8-9 Oct. 1992 in Mainz, Germany are included. Topics covered include: a backscatter Moessbauer spectrometer (BaMS) for use on Mars; database of proposed payloads and instruments for SEI missions; determination of martian soil mineralogy and water content using the Thermal Analyzer for Planetary Soils (TAPS); in situ identification of the martian surface material and its interaction with the martian atmosphere using DTA/GC; mass spectrometer-pyrolysis experiment for atmospheric and soil sample analysis on the surface of Mars; and optical luminescence spectroscopy as a probe of the surface mineralogy of Mars.

Geotechnical centrifuge under construction

NASA Astrophysics Data System (ADS)

Richman, Barbara T.

Modifications are underway at the National Aeronautics and Space Administration (NASA) Ames Research Center in California to transform a centrifuge used in the Apollo space program to the largest geotechnical centrifuge in the free world. The centrifuge, to be finished in August and opened next January, following check out and tuning, will enable geoscientists to model stratigraphic features down to 275 m below the earth's surface. Scientists will be able to model processes that are coupled with body force loading, including earthquake response of earth structures and soil structure interaction; rubbled-bed behavior during in situ coal gasification or in oil shale in situ retorts; behavior of frozen soil; frost heave; behavior of offshore structures; wave-seabed interactions; explosive cratering; and blast-induced liquefaction.The centrifuge will have a load capacity of 900-g-tons (short); that is, it will be able to carry a net soil load of 3 short tons to a centripetal acceleration of 300 times the acceleration caused by gravity. Modified for a total cost of $2.4 million, the centrifuge will have an arm with a 7.6-m radius and a swinging platform or bucket at its end that will be able to carry a payload container measuring 2.1×2.1 m. An additional future input of $500,000 would enable the purchase of a larger bucket that could accommodate a load of up to 20 tons, according to Charles Babendreier, program director for geotechnical engineering at the National Science Foundation. Additional cooling for the motor would also be required. The centrifuge has the capability of accelerating the 20-ton load to 100 g.

Vadose zone process that control landslide initiation and debris flow propagation

NASA Astrophysics Data System (ADS)

Sidle, Roy C.

2015-04-01

Advances in the areas of geotechnical engineering, hydrology, mineralogy, geomorphology, geology, and biology have individually advanced our understanding of factors affecting slope stability; however, the interactions among these processes and attributes as they affect the initiation and propagation of landslides and debris flows are not well understood. Here the importance of interactive vadose zone processes is emphasized related to the mechanisms, initiation, mode, and timing of rainfall-initiated landslides that are triggered by positive pore water accretion, loss of soil suction and increase in overburden weight, and long-term cumulative rain water infiltration. Both large- and small-scale preferential flow pathways can both contribute to and mitigate instability, by respectively concentrating and dispersing subsurface flow. These mechanisms are influenced by soil structure, lithology, landforms, and biota. Conditions conducive to landslide initiation by infiltration versus exfiltration are discussed relative to bedrock structure and joints. The effects of rhizosphere processes on slope stability are examined, including root reinforcement of soil mantles, evapotranspiration, and how root structures affect preferential flow paths. At a larger scale, the nexus between hillslope landslides and in-channel debris flows is examined with emphasis on understanding the timing of debris flows relative to chronic and episodic infilling processes, as well as the episodic nature of large rainfall and related stormflow generation in headwater streams. The hydrogeomorphic processes and conditions that determine whether or not landslides immediately mobilize into debris flows is important for predicting the timing and extent of devastating debris flow runout in steep terrain. Given the spatial footprint of individual landslides, it is necessary to assess vadose zone processes at appropriate scales to ascertain impacts on mass wasting phenomena. Articulating the appropriate level of detail of small-scale vadose zone processes into landslide models is a particular challenge. As such, understanding flow pathways in regoliths susceptible to mass movement is critical, including distinguishing between conditions conducive to vertical recharge of water through relatively homogeneous soil mantles and conditions where preferential flow dominates - either by rapid infiltration and lateral flow through interconnected preferential flow networks or via exfiltration through bedrock fractures. These different hydrologic scenarios have major implications for the occurrence, timing, and mode of slope failures.

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions.

PubMed

Ceapă, Corina Diana; Vázquez-Hernández, Melissa; Rodríguez-Luna, Stefany Daniela; Cruz Vázquez, Angélica Patricia; Jiménez Suárez, Verónica; Rodríguez-Sanoja, Romina; Alvarez-Buylla, Elena R; Sánchez, Sergio

2018-01-01

Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions.

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions

PubMed Central

Rodríguez-Luna, Stefany Daniela; Cruz Vázquez, Angélica Patricia; Jiménez Suárez, Verónica; Rodríguez-Sanoja, Romina; Alvarez-Buylla, Elena R.; Sánchez, Sergio

2018-01-01

Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions. PMID:29447216

Creating deep soil core monoliths: Beyond the solum

USDA-ARS?s Scientific Manuscript database

Soil monoliths serve as useful teaching aids in the study of the Earth’s critical zone where rock, soil, water, air, and organisms interact. Typical monolith preparation has so far been confined to the 1 to 2-m depth of the solum. Critical ecosystem services provided by soils include materials from ...

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.

Soil fauna responses to natural disturbances, invasive species, and global climate change: Current state of the science and a call to action

Treesearch

David R. Coyle; Uma J. Nagendra; Melanie K. Taylor; J. Holly Campbell; Chelsea E. Cunard; Aaron H. Joslin; Abha Mundepi; Carly A. Phillips; Mac A. Callaham

2017-01-01

Environmental disturbances seem to be increasing in frequency and impact, yet we have little understanding of the belowground impacts of these events. Soil fauna, while widely acknowledged to be important drivers of biogeochemical function, soil structure and sustainability, and trophic interactions, are understudied compared to other belowground organisms such as...

Greatest soil microbial diversity found in micro-habitats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

Dig It! The Secrets of Soil

Science.gov Websites

It! The Secrets of Soil Come and Explore! Discover the amazing world of soils with images and information from the Dig It! The Secrets of Soil exhibit from the Smithsonian's National Museum of Natural and new web content will be added over the coming months including a new soil blog. New Interactives

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

PubMed

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces.

PubMed

Wang, Haitao; Cheng, Minying; Dsouza, Melissa; Weisenhorn, Pamela; Zheng, Tianling; Gilbert, Jack A

2018-05-01

Urban greenspaces provide extensive ecosystem services, including pollutant remediation, water management, carbon maintenance, and nutrient cycling. However, while the urban soil microbiota underpin these services, we still have limited understanding of the factors that influence their distribution. We characterized soil bacterial communities from turf-grasses associated with urban parks, streets, and residential sites across a major urban environment, including a gradient of human population density. Bacterial diversity was significantly positively correlated with the population density; and species diversity was greater in park and street soils, compared to residential soils. Population density and greenspace type also led to significant differences in the microbial community composition that was also significantly correlated with soil pH, moisture, and texture. Co-occurrence network analysis revealed that microbial guilds in urban soils were well correlated. Abundant soil microbes in high density population areas had fewer interactions, while abundant bacteria in high moisture soils had more interactions. These results indicate the significant influence of changes in urban demographics and land-use on soil microbial communities. As urbanization is rapidly growing across the planet, it is important to improve our understanding of the consequences of urban zoning on the soil microbiota.

[Effects of biochar on microbial ecology in agriculture soil: a review].

PubMed

Ding, Yan-Li; Liu, Jie; Wang, Ying-Ying

2013-11-01

Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.

First and Higher Order Effects on Zero Order Radiative Transfer Model

NASA Astrophysics Data System (ADS)

Neelam, M.; Mohanty, B.

2014-12-01

Microwave radiative transfer model are valuable tool in understanding the complex land surface interactions. Past literature has largely focused on local sensitivity analysis for factor priotization and ignoring the interactions between the variables and uncertainties around them. Since land surface interactions are largely nonlinear, there always exist uncertainties, heterogeneities and interactions thus it is important to quantify them to draw accurate conclusions. In this effort, we used global sensitivity analysis to address the issues of variable uncertainty, higher order interactions, factor priotization and factor fixing for zero-order radiative transfer (ZRT) model. With the to-be-launched Soil Moisture Active Passive (SMAP) mission of NASA, it is very important to have a complete understanding of ZRT for soil moisture retrieval to direct future research and cal/val field campaigns. This is a first attempt to use GSA technique to quantify first order and higher order effects on brightness temperature from ZRT model. Our analyses reflect conditions observed during the growing agricultural season for corn and soybeans in two different regions in - Iowa, U.S.A and Winnipeg, Canada. We found that for corn fields in Iowa, there exist significant second order interactions between soil moisture, surface roughness parameters (RMS height and correlation length) and vegetation parameters (vegetation water content, structure and scattering albedo), whereas in Winnipeg, second order interactions are mainly due to soil moisture and vegetation parameters. But for soybean fields in both Iowa and Winnipeg, we found significant interactions only to exist between soil moisture and surface roughness parameters.

Finite element modeling of a shaking table test to evaluate the dynamic behaviour of a soil-foundation system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abate, G.; Massimino, M. R.; Maugeri, M.

The deep investigation of soil-foundation interaction behaviour during earthquakes represent one of the key-point for a right seismic design of structures, which can really behave well during earthquake, avoiding dangerous boundary conditions, such as weak foundations supporting the superstructures. The paper presents the results of the FEM modeling of a shaking table test involving a concrete shallow foundation resting on a Leighton Buzzard sand deposit. The numerical simulation is performed using a cap-hardening elasto-plastic constitutive model for the soil and specific soil-foundation contacts to allow slipping and up-lifting phenomena. Thanks to the comparison between experimental and numerical results, the powermore » and the limits of the proposed numerical model are focused. Some aspects of the dynamic soil-foundation interaction are also pointed out.« less

Effects of drought on forest soil structure and hydrological soil functions

NASA Astrophysics Data System (ADS)

Gimbel, K.; Puhlmann, H.; Weiler, M.

2012-04-01

Climate change is predicted to severely affect precipitation patterns across central Europe. Soil structure is closely linked to the activity of soil microbiota and plant roots, which modify flow pathways along roots, organic matter and water repellence of soils. Through shrinkage and fracturing of soil aggregates, soil structure is also responding to changing climate (in particular drought) conditions. We investigate the possible effects on biogeochemical and hydropedological processes in response to predicted future reduced precipitation, and the interaction of these processes with the biodiversity of the forest understorey and soil biota. The hypotheses of this study are: (i) drought causes a change in soil structure, which affects hydrological soil functions (water infiltration, uptake and redistribution); (ii) changes in rooting patterns and microbial community composition, in response to drought, influence the hydrological soil functions. To test our hypotheses, we built adaptive roofing systems on nine sites in Germany, which allow a flexible reduction of precipitation in order to achieve the long-term minimum precipitation of a site. Here we present first measurements of our repeated measuring/sampling campaign, which will be conducted over a period of three years. The aim of our experiments is to analyze soil pore architecture and related flow and transport behaviour with dye tracer sprinkling experiments, soil column experiments with stable isotope (deuterium, oxygen-18) enriched water, computed tomography at soil monoliths (~70 l) and multi-step outflow experiments with 100 ml soil cores. Finally, we sketch our idea how to relate the observed temporal changes of soil structure and hydrological soil functions to the observed dynamics of hydrometeorological site conditions, soil moisture and desiccation as well as changes in rooting patterns, herb layer and soil microbiotic communities. The results of this study may help to assess future behavior of the plant-soil-water-microbiology-system and may help to adjust models to predict future response to different precipitation patterns as well as help coping with existing and future emerging challenges in forest management.

The Effect of Vegetation on Soil Water Infiltration and Retention Capacity by Improving Soil Physiochemical Property in Semi-arid Grassland

NASA Astrophysics Data System (ADS)

A, Y.; Wang, G.

2017-12-01

Water shortage is the main limiting factor for semi-arid grassland development. However, the grassland are gradually degraded represented by species conversion, biomass decrease and ecosystem structure simplification under the influence of human activity. Soil water characteristics such as moisture, infiltration and conductivity are critical variables affecting the interactions between soil parameters and vegetation. In this study, Cover, Height, Shannon-Wiener diversity index, Pielou evenness index and Richness index are served as indexes of vegetation productivity and community structure. And saturated hydraulic conductivity (Ks) and soil moisture content are served as indexes of soil water characters. The interaction between vegetation and soil water is investigated through other soil parameters, such as soil organic matter content at different vertical depths and in different degradation area (e.g., initial, transition and degraded plots). The results show that Ks significantly controlled by soil texture other than soil organic matter content. So the influence of vegetation on Ks through increasing soil organic content (SOM) might be slight. However, soil moisture content (SMC) appeared significantly positive relationship with SOM and silt content and negative relationship with sand content at all depth, significantly. This indicated that capacity of soil water storage was influenced both by soil texture and organic matter. In addition, the highest correlation coefficient of SMC was with SOM at the sub-surficial soil layer (20 40 cm). At the depth of 20 40 cm, the soil water content was relatively steady which slightly influenced by precipitation and evaporation. But it significantly influenced by soil organic matter content which related to vegetation. The correlation coefficient between SOM and SMC at topsoil layer (0 20 cm) was lowest (R2=0.36, p<0.01), which indicated the influence of vegetation on soil water content not only by soil organic matter content but also the other influential factors, such as the root water uptake, precipitation and evaporation.

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

Observing and modeling links between soil moisture, microbes and CH4 fluxes from forest soils

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Levy-Booth, David; Barker, Jason; Prescott, Cindy; Grayston, Sue

2017-04-01

Soil moisture is a key driver of methane (CH4) fluxes in forest soils, both of the net uptake of atmospheric CH4 and emission from the soil. Climate and land use change will alter spatial patterns of soil moisture as well as temporal variability impacting the net CH4 exchange. The impact on the resultant net CH4 exchange however is linked to the underlying spatial and temporal distribution of the soil microbial communities involved in CH4 cycling as well as the response of the soil microbial community to environmental changes. Significant progress has been made to target specific CH4 consuming and producing soil organisms, which is invaluable in order to understand the microbial regulation of the CH4 cycle in forest soils. However, it is not clear as to which extent soil moisture shapes the structure, function and abundance of CH4 specific microorganisms and how this is linked to observed net CH4 exchange under contrasting soil moisture regimes. Here we report on the results from a research project aiming to understand how the CH4 net exchange is shaped by the interactive effects soil moisture and the spatial distribution CH4 consuming (methanotrophs) and producing (methanogens). We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs and methanogens, soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient in a temperate rainforest on the Canadian Pacific coast. Furthermore, we conducted laboratory experiments to determine whether the net CH4 exchange from hydrologically contrasting forest soils responded differently to changes in soil moisture. Lastly, we modelled the microbial mediation of net CH4 exchange along the soil moisture gradient using structural equation modeling. Our study shows that it is possible to link spatial patterns of in situ net exchange of CH4 to microbial abundance of CH4 consuming and producing organisms. We also show that the microbial community responds different to environmental change dependent on the soil moisture regime. These results are important to include in future modeling efforts to predict changes in soil-atmosphere exchange of CH4 under global change.

Complexes of the antimicrobial ciprofloxacin with soil, peat, and aquatic humic substances.

PubMed

Aristilde, Ludmilla; Sposito, Garrison

2013-07-01

Natural organic matter (NOM) is implicated in the binding of antibiotics by particles in soils and waters. The authors' previous computational study revealed structural rearrangement of both hydrophilic and hydrophobic moieties of NOM to favor H-bonding and other intermolecular interactions, as well as both competition with ion-exchange reactions and bridging interactions by NOM-bound divalent cations. The importance of these interactions was investigated using fluorescence-quenching spectroscopy to study the adsorption of ciprofloxacin (Cipro), a fluoroquinolone antibiotic, on 4 reference humic substances (HSs): Elliott soil humic acid (HA), Pahokee peat HA, and Suwannee river HA and fulvic acid. A simple affinity spectrum HS model was developed to characterize the cation-exchange capacity and the amount of H-bond donor moieties as a function of pH. The adsorption results stress the influence of both pH conditions and the type of HS: both soil HA and peat HA exhibited up to 3 times higher sorption capacity than the aquatic HS at pH ≥ 6, normalizing to the aromatic C content accounted for the differences among the terrestrial HS, and increasing the concentration of divalent cations led to a decrease in adsorption on aquatic HA but not on soil HA. In addition, the pH-dependent speciation models of the Cipro-HS complexes illustrate an increase in complexation due to an increase in deprotonation of HS ligands with increasing pH and, at circumneutral and alkaline pH, enhanced complexation of zwitterionic Cipro only in the presence of soil HA and peat HA. The findings of the present study imply that, in addition to electrostatic interactions, van der Waals interactions as facilitated by aromatic structures and H-bond donating moieties in terrestrial HS may facilitate a favorable binding environment. Environ Toxicol Chem 2013;32:1467-1478. © 2013 SETAC. Copyright © 2013 SETAC.

Transformation of soil microbial community structure in response to anaerobic soil disinfestation for soil-borne disease control in strawberry

USDA-ARS?s Scientific Manuscript database

Anaerobic soil disinfestation (ASD) has been used to control soil-borne pathogens and nematodes in various plant production systems including strawberries. Disease control is commonly attributed to the depletion of oxygen and the generation of toxic compounds, including organic acids and volatiles....

Performance-based seismic assessment of skewed bridges with and without considering soil-foundation interaction effects for various site classes

NASA Astrophysics Data System (ADS)

Ghotbi, Abdoul R.

2014-09-01

The seismic behavior of skewed bridges has not been well studied compared to straight bridges. Skewed bridges have shown extensive damage, especially due to deck rotation, shear keys failure, abutment unseating and column-bent drift. This research, therefore, aims to study the behavior of skewed and straight highway overpass bridges both with and without taking into account the effects of Soil-Structure Interaction (SSI) due to near-fault ground motions. Due to several sources of uncertainty associated with the ground motions, soil and structure, a probabilistic approach is needed. Thus, a probabilistic methodology similar to the one developed by the Pacific Earthquake Engineering Research Center (PEER) has been utilized to assess the probability of damage due to various levels of shaking using appropriate intensity measures with minimum dispersions. The probabilistic analyses were performed for various bridge configurations and site conditions, including sand ranging from loose to dense and clay ranging from soft to stiff, in order to evaluate the effects. The results proved a considerable susceptibility of skewed bridges to deck rotation and shear keys displacement. It was also found that SSI had a decreasing effect on the damage probability for various demands compared to the fixed-base model without including SSI. However, deck rotation for all types of the soil and also abutment unseating for very loose sand and soft clay showed an increase in damage probability compared to the fixed-base model. The damage probability for various demands has also been found to decrease with an increase of soil strength for both sandy and clayey sites. With respect to the variations in the skew angle, an increase in skew angle has had an increasing effect on the amplitude of the seismic response for various demands. Deck rotation has been very sensitive to the increase in the skew angle; therefore, as the skew angle increased, the deck rotation responded accordingly. Furthermore, abutment unseating showed an increasing trend due to an increase in skew angle for both fixed-base and SSI models.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

PubMed

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2015-03-20

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

From patterns to causal understanding: Structural equation modeling (SEM) in soil ecology

USGS Publications Warehouse

Eisenhauer, Nico; Powell, Jeff R; Grace, James B.; Bowker, Matthew A.

2015-01-01

In this perspectives paper we highlight a heretofore underused statistical method in soil ecological research, structural equation modeling (SEM). SEM is commonly used in the general ecological literature to develop causal understanding from observational data, but has been more slowly adopted by soil ecologists. We provide some basic information on the many advantages and possibilities associated with using SEM and provide some examples of how SEM can be used by soil ecologists to shift focus from describing patterns to developing causal understanding and inspiring new types of experimental tests. SEM is a promising tool to aid the growth of soil ecology as a discipline, particularly by supporting research that is increasingly hypothesis-driven and interdisciplinary, thus shining light into the black box of interactions belowground.

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

PubMed Central

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

Rich in life but poor in data: the known knowns and known unknowns of modelling how soil biology drives soil structure

NASA Astrophysics Data System (ADS)

Hallett, Paul; Ogden, Mike

2015-04-01

Soil biology has a fascinating capacity to manipulate pore structure by altering or overcoming hydrological and mechanical properties of soil. Many have postulated, quite rightly, that this capacity of soil biology to 'engineer' its habitat drives its diversity, improves competitiveness and increases resilience to external stresses. A large body of observational research has quantified pore structure evolution accompanied by the growth of organisms in soil. Specific compounds that are exuded by organisms or the biological structures they create have been isolated and found to correlate well with observed changes to pore structure or soil stability. This presentation will provide an overview of basic mechanical and hydrological properties of soil that are affected by biology, and consider missing data that are essential to model how they impact soil structure evolution. Major knowledge gaps that prevent progress will be identified and suggestions will be made of how research in this area should progress. We call for more research to gain a process based understanding of structure formation by biology, to complement observational studies of soil structure before and after imposed biological activity. Significant advancement has already been made in modelling soil stabilisation by plant roots, by combining data on root biomechanics, root-soil interactions and soil mechanical properties. Approaches for this work were developed from earlier materials science and geotechnical engineering research, and the same ethos should be adopted to model the impacts of other biological compounds. Fungal hyphae likely reinforce soils in a similar way to plant roots, with successful biomechanical measurements of these micron diameter structures achieved with micromechanical test frames. Extending root reinforcement models to fungi would not be a straightforward exercise, however, as interparticle bonding and changes to pore water caused by fungal exudates could have a major impact on structure formation and stability. Biological exudates from fungi, bacteria or roots have been found to decrease surface tension and increase viscosity of pore water, with observed impacts to soil strength and water retention. Modelling approaches developed in granular mechanics and geotechnical engineering could be built upon to incorporate biological transformations of hydrological and mechanical properties of soil. With new testing approaches, adapted from materials science, pore scale hydromechanical impacts from biological exudates can be quantified. The research can be complemented with model organisms with differences in biological structures (e.g. root hair mutants), exudation or other properties. Coupled with technological advances that provide 4D imaging of soil structure at relatively rapid capture rates, the potential opportunities to disentangle and model how biology drives soil structure evolution and stability are vast. By quantifying basic soil hydrological and mechanical processes that are driven by soil biology, unknown unknowns may also emerge, providing new insight into how soils function.

Direct and indirect effects of climate change on amphibian populations

USGS Publications Warehouse

Blaustein, Andrew R.; Walls, Susan C.; Bancroft, Betsy A.; Lawler, Joshua J.; Searle, Catherine L.; Gervasi, Stephanie S.

2010-01-01

As part of an overall decline in biodiversity, populations of many organisms are declining and species are being lost at unprecedented rates around the world. This includes many populations and species of amphibians. Although numerous factors are affecting amphibian populations, we show potential direct and indirect effects of climate change on amphibians at the individual, population and community level. Shifts in amphibian ranges are predicted. Changes in climate may affect survival, growth, reproduction and dispersal capabilities. Moreover, climate change can alter amphibian habitats including vegetation, soil, and hydrology. Climate change can influence food availability, predator-prey relationships and competitive interactions which can alter community structure. Climate change can also alter pathogen-host dynamics and greatly influence how diseases are manifested. Changes in climate can interact with other stressors such as UV-B radiation and contaminants. The interactions among all these factors are complex and are probably driving some amphibian population declines and extinctions.

Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential

PubMed Central

Haldar, Shyamalina; Sengupta, Sanghamitra

2015-01-01

Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration. PMID:25926899

Sorption mechanism of enrofloxacin on humic acids extracted from Brazilian soils.

PubMed

Martínez-Mejía, Mónica J; Sato, Isabela; Rath, Susanne

2017-07-01

Veterinary antimicrobials are emerging environmental contaminants of concern. In this study, the sorption of enrofloxacin (ENR) onto humic acids (HAs) extracted from three Brazilian soils was evaluated. HAs were characterized by elemental analysis and solid 13 C nuclear magnetic resonance spectroscopy. The sorption of ENR onto HAs was at least 20-fold higher than onto the soils from which they were separated. Ionic and cation bridging are the primary interactions involved. The interactions driven by cation exchange are predominant on HAs, which appear to have abundant carboxylic groups and a relatively high proportion of H-bond donor moieties with carbohydrate-like structures. Interactions explained by cation bridging and/or surface complexation on HAs are facilitated by moieties containing conjugated ligands, significant content of oxygen-containing functional groups, such as phenolic-OH or lignin-like structures. HAs containing electron-donating phenolic moieties and carboxylic acid ligand groups exhibit a sorption mechanism that is primarily driven by strong metal binding, favoring the formation of ternary complexes between functional groups of the organic matter and drugs.

Soil cover of gas-bearing areas

NASA Astrophysics Data System (ADS)

Mozharova, N. V.

2010-08-01

Natural soils with disturbed functioning parameters compared to the background soils with conservative technogenic-pedogenic features were distinguished on vast areas above the artificial underground gas storages in the zones of spreading and predominant impact of hydrocarbon gases. The disturbance of the functioning parameters is related to the increase in the methane concentration, the bacterial oxidation intensity and destruction, and the complex microbiological and physicochemical synthesis of iron oxides. The technogenic-pedogenic features include neoformations of bacteriomorphic microdispersed iron oxides. The impurity components consist of elements typical for biogenic structures. New soil layers, horizons, specific anthropogenically modified soils, and soil-like structures were formed on small areas in the industrial zones of underground gas storages due to the mechanical disturbance, the deposition of drilling sludge, and the chemical contamination. Among the soils, postlithogenic formations were identified—chemotechnosols (soddy-podzolic soils and chernozems), as well as synlithogenic ones: strato-chemotechnosols and stratochemoembryozems. The soil-like bodies included postlithogenic soil-like structures (chemotechnozems) and synlithogenic ones (strato-chemotechnozems). A substantive approach was used for the soil diagnostics. The morphological and magnetic profiles and the physical, chemical, and physicochemical properties of the soils were analyzed. The micromorphological composition of the soil magnetic fraction was used as a magnetic label.

Three dimensional, non-linear, finite element analysis of compactable soil interaction with a hyperelastic wheel

NASA Astrophysics Data System (ADS)

Chiroux, Robert Charles

The objective of this research was to produce a three dimensional, non-linear, dynamic simulation of the interaction between a hyperelastic wheel rolling over compactable soil. The finite element models developed to produce the simulation utilized the ABAQUS/Explicit computer code. Within the simulation two separate bodies were modeled, the hyperelastic wheel and a compactable soil-bed. Interaction between the bodies was achieved by allowing them to come in contact but not to penetrate the contact surface. The simulation included dynamic loading of a hyperelastic, rubber tire in contact with compactable soil with an applied constant angular velocity or torque, including a tow load, applied to the wheel hub. The constraints on the wheel model produced a straight and curved path. In addition the simulation included a shear limit between the tire and soil allowing for the introduction of slip. Soil properties were simulated using the Drucker-Prager, Cap Plasticity model available within the ABAQUS/Explicit program. Numerical results obtained from the three dimensional model were compared with related experimental data and showed good correlation for similar conditions. Numerical and experimental data compared well for both stress and wheel rut formation depth under a weight of 5.8 kN and a constant angular velocity applied to the wheel hub. The simulation results provided a demonstration of the benefit of three-dimensional simulation in comparison to previous two-dimensional, plane strain simulations.

Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient.

PubMed

Collins, Courtney G; Stajich, Jason E; Weber, Sören E; Pombubpa, Nuttapon; Diez, Jeffrey M

2018-04-19

Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function; however, our understanding of alpine soil ecology remains limited. This study aimed to (i) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to (ii) assess the impact of woody shrub expansion on these patterns. In the White Mountains of California, sagebrush (Artemisia rothrockii) shrubs have been expanding upwards into alpine areas since 1960. In this study, we combined observational field data with a manipulative shrub removal experiment along an elevation transect of alpine shrub expansion. We utilized next-generation sequencing of the ITS1 region for fungi and joint distribution modelling to tease apart effects of the environment and intracommunity interactions on soil fungi. We found that soil fungal diversity declines and community composition changes with increasing elevation. Both abiotic factors (primarily soil moisture and soil organic C) and woody sagebrush range expansion had significant effects on these patterns. However, fungal diversity and relative abundance had high spatial variation, overwhelming the predictive power of vegetation type, elevation and abiotic soil conditions at the landscape scale. Finally, we observed positive and negative associations among fungal taxa which may be important in structuring community responses to global change. © 2018 John Wiley & Sons Ltd.

Separating the role of biotic interactions and climate in determining adaptive response of plants to climate change.

PubMed

Tomiolo, Sara; Van der Putten, Wim H; Tielbörger, Katja

2015-05-01

Altered rainfall regimes will greatly affect the response of plant species to climate change. However, little is known about how direct effects of changing precipitation on plant performance may depend on other abiotic factors and biotic interactions. We used reciprocal transplants between climatically very different sites with simultaneous manipulation of soil, plant population origin, and neighbor conditions to evaluate local adaptation and possible adaptive response of four Eastern Mediterranean annual plant species to climate change. The effect of site on plant performance was negligible, but soil origin had a strong effect on fecundity, most likely due to differential water retaining ability. Competition by neighbors strongly reduced fitness. We separated the effects of the abiotic and biotic soil properties on plant performance by repeating the field experiment in a greenhouse under homogenous environmental conditions and including a soil biota manipulation treatment. As in the field, plant performance differed among soil origins and neighbor treatments. Moreover, we found plant species-specific responses to soil biota that may be best explained by the differential sensitivity to negative and positive soil biota effects. Overall, under the conditions of our experiment with two contrasting sites, biotic interactions had a strong effect on plant fitness that interacted with and eventually overrode climate. Because climate and biotic interactions covary, reciprocal transplants and climate gradient studies should consider soil biotic interactions and abiotic conditions when evaluating climate change effects on plant performance.

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-10-01

Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions. Copyright © 2016. Published by Elsevier B.V.

Microscopic and spectroscopic characterization of humic substances from a compost amended copper contaminated soil: main features and their potential effects on Cu immobilization.

PubMed

Medina, Jorge; Monreal, Carlos; Chabot, Denise; Meier, Sebastián; González, María Eugenia; Morales, Esteban; Parillo, Rita; Borie, Fernando; Cornejo, Pablo

2017-06-01

We characterized humic substances (HS) extracted from a Cu-contaminated soil without compost addition (C) or amended with a wheat straw-based compost (WSC) (H1), co-composted with Fe 2 O 3 (H2), or co-composted with an allophane-rich soil (H3). Extracted HS were characterized under electron microscopy (SEM/TEM), energy-dispersive X-ray (X-EDS), and Fourier transform infrared (FTIR) spectroscopy. In addition, HS extracted from WSC (H4) were characterized at pH 4.0 and 8.0 with descriptive purposes. At pH 4.0, globular structures of H4 were observed, some of them aggregating within a large network. Contrariwise, at pH 8.0, long tubular and disaggregated structures prevailed. TEM microscopy suggests organo-mineral interactions at scales of 1 to 200 nm with iron oxide nanoparticles. HS extracted from soil-compost incubations showed interactions at nanoscale with minerals and crystal compounds into the organic matrix of HS. Bands associated to acidic functional groups of HS may suggest potential sorption interactions with transition metals. We conclude that metal ions and pH have an important role controlling the morphology and configuration of HS from WSC. Characterization of H4 extracted from WSC showed that physicochemical protection of HS could be present in composting systems treated with inorganic materials. Finally, the humified fractions obtained from compost-amended soils may have an important effect on metal-retention, supporting their potential use in metal-contaminated soils.

Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xue, Kai; Yuan, Mengting M.; Xie, Jianping

Clipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties and plant and microbial communities, in particular, on microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C4 peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. Withmore » less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38% to 137% in response to either clipping or the combined treatment, which could weaken long-term soil carbon stability and trigger positive feedback with respect to warming. Clipping alone also increased the abundance of genes for nitrogen fixation, mineralization, and denitrification by 32% to 39%. Such potentially stimulated nitrogen fixation could help compensate for the 20% decline in soil ammonium levels caused by clipping alone and could contribute to unchanged plant biomass levels. Moreover, clipping tended to interact antagonistically with warming, especially with respect to effects on nitrogen cycling genes, demonstrating that single-factor studies cannot predict multifactorial changes. These results revealed that clipping alone or in combination with warming altered soil and plant properties as well as the abundance and structure of soil microbial functional genes. Aboveground biomass removal for biofuel production needs to be reconsidered, as the long-term soil carbon stability may be weakened. IMPORTANCE Global change involves simultaneous alterations, including those caused by climate warming and land management practices (e.g., clipping). Data on the interactive effects of warming and clipping on ecosystems remain elusive, particularly in microbial ecology. This study found that clipping alters microbial responses to warming and demonstrated the effects of antagonistic interactions between clipping and warming on microbial functional genes. Clipping alone or combined with warming enriched genes degrading relatively recalcitrant carbon, likely reflecting the decreased quantity of soil carbon input from litter, which could weaken long-term soil C stability and trigger positive warming feedback. These results have important implications in assessing and predicting the consequences of global climate change and indicate that the removal of aboveground biomass for biofuel production may need to be reconsidered.« less

Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming

DOE PAGES

Xue, Kai; Yuan, Mengting M.; Xie, Jianping; ...

2016-09-27

Clipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties and plant and microbial communities, in particular, on microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C4 peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. Withmore » less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38% to 137% in response to either clipping or the combined treatment, which could weaken long-term soil carbon stability and trigger positive feedback with respect to warming. Clipping alone also increased the abundance of genes for nitrogen fixation, mineralization, and denitrification by 32% to 39%. Such potentially stimulated nitrogen fixation could help compensate for the 20% decline in soil ammonium levels caused by clipping alone and could contribute to unchanged plant biomass levels. Moreover, clipping tended to interact antagonistically with warming, especially with respect to effects on nitrogen cycling genes, demonstrating that single-factor studies cannot predict multifactorial changes. These results revealed that clipping alone or in combination with warming altered soil and plant properties as well as the abundance and structure of soil microbial functional genes. Aboveground biomass removal for biofuel production needs to be reconsidered, as the long-term soil carbon stability may be weakened. IMPORTANCE Global change involves simultaneous alterations, including those caused by climate warming and land management practices (e.g., clipping). Data on the interactive effects of warming and clipping on ecosystems remain elusive, particularly in microbial ecology. This study found that clipping alters microbial responses to warming and demonstrated the effects of antagonistic interactions between clipping and warming on microbial functional genes. Clipping alone or combined with warming enriched genes degrading relatively recalcitrant carbon, likely reflecting the decreased quantity of soil carbon input from litter, which could weaken long-term soil C stability and trigger positive warming feedback. These results have important implications in assessing and predicting the consequences of global climate change and indicate that the removal of aboveground biomass for biofuel production may need to be reconsidered.« less

Geographical ecology of the palms (Arecaceae): determinants of diversity and distributions across spatial scales

PubMed Central

Eiserhardt, Wolf L.; Svenning, Jens-Christian; Kissling, W. Daniel; Balslev, Henrik

2011-01-01

Background The palm family occurs in all tropical and sub-tropical regions of the world. Palms are of high ecological and economical importance, and display complex spatial patterns of species distributions and diversity. Scope This review summarizes empirical evidence for factors that determine palm species distributions, community composition and species richness such as the abiotic environment (climate, soil chemistry, hydrology and topography), the biotic environment (vegetation structure and species interactions) and dispersal. The importance of contemporary vs. historical impacts of these factors and the scale at which they function is discussed. Finally a hierarchical scale framework is developed to guide predictor selection for future studies. Conclusions Determinants of palm distributions, composition and richness vary with spatial scale. For species distributions, climate appears to be important at landscape and broader scales, soil, topography and vegetation at landscape and local scales, hydrology at local scales, and dispersal at all scales. For community composition, soil appears important at regional and finer scales, hydrology, topography and vegetation at landscape and local scales, and dispersal again at all scales. For species richness, climate and dispersal appear to be important at continental to global scales, soil at landscape and broader scales, and topography at landscape and finer scales. Some scale–predictor combinations have not been studied or deserve further attention, e.g. climate on regional to finer scales, and hydrology and topography on landscape and broader scales. The importance of biotic interactions – apart from general vegetation structure effects – for the geographic ecology of palms is generally underexplored. Future studies should target scale–predictor combinations and geographic domains not studied yet. To avoid biased inference, one should ideally include at least all predictors previously found important at the spatial scale of investigation. PMID:21712297

Vertical variation of a black soil's properties in response to freeze-thaw cycles and its links to shift of microbial community structure.

PubMed

Han, Ziming; Deng, Mingwen; Yuan, Anqi; Wang, Jiahui; Li, Hao; Ma, Jincai

2018-06-01

Soil freeze-thaw cycles (FTCs) change soil physical, chemical, and biological properties, however information regarding their vertical variations in response to FTCs is limited. In this work, black soil (silty loam) packed soil columns were exposed to 8 FTCs, and soil properties were determined for each of vertical layer of soil columns. The results revealed that after FTCs treatment, moisture and electrical conductivity (EC) salinity tended to increase in upper soil layers. Increments of ammonium nitrogen (NH 4 + -N) and nitrate nitrogen (NO 3 - -N) in top layers (0-10cm) were greater than those in other layers, and increments of water soluble organic carbon (WSOC) and decrease of microbial biomass carbon (MBC) in middle layers (10-20cm) were greater than those in both ends. Overall, microbial community structure was mainly influenced by soil physical properties (moisture and EC) and chemical properties (pH and WSOC). For bacterial (archaeal) and fungal communities, soil physical properties, chemical properties and their interaction explained 79.73% and 82.66% of total variation, respectively. Our results provided insights into the vertical variation of soil properties caused by FTCs, and such variation had a major impact on the change of structure and composition of soil bacterial and fungal communities. Copyright © 2017 Elsevier B.V. All rights reserved.

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community.

PubMed

Hortal, S; Lozano, Y M; Bastida, F; Armas, C; Moreno, J L; Garcia, C; Pugnaire, F I

2017-12-19

Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.

Soil biota effects on clonal growth and flowering in the forest herb Stachys sylvatica

NASA Astrophysics Data System (ADS)

de la Peña, Eduardo; Bonte, Dries

2011-03-01

The composition of a soil community can vary drastically at extremely short distances. Therefore, plants from any given population can be expected to experience strong differences in belowground biotic interactions. Although it is well recognized that the soil biota plays a significant role in the structure and dynamics of plant communities, plastic responses in growth strategies as a function of soil biotic interactions have received little attention. In this study, we question whether the biotic soil context from two forest associated contrasting environments (the forest understory and the hedgerows) determines the balance between clonal growth and flowering of the perennial Stachys sylvatica. Using artificial soils, we compared the growth responses of this species following inoculation with the mycorrhizal and microbial community extracted either from rhizospheric soil of the forest understory or from the hedgerows. The microbial context had a strong effect on plant functional traits, determining the production of runners and inflorescences. Plants inoculated with the hedgerow community had a greater biomass, larger number of runners, and lower resource investment in flower production than was seen in plants inoculated with the understory microbial community. The obtained results illustrate that belowground biotic interactions are essential to understand basic plastic growth responses determinant for plant establishment and survival. The interactions with microbial communities from two contrasting habitats resulted in two different, and presumably adaptive, growth strategies that were optimal for the conditions prevalent in the environments compared; and they are as such an essential factor to understand plant-plant, plant-animal interactions and the dispersal capacities of clonal plants.

Lignin biochemistry and soil N determine crop residue decomposition and soil priming

USDA-ARS?s Scientific Manuscript database

Cropping history can affect soil properties, including available N, but little is known about the interactive effects of residue biochemistry, temperature and cropping history on residue decomposition. A laboratory incubation examined the role of residue biochemistry and temperature on the decomposi...

Advances in understanding the molecular structure of soil organic matter: Implications for interactions in the environment

EPA Science Inventory

We take a historic approach to explore how concepts of the chemical and physical nature of soil organic matter have evolved over time. We emphasize conceptual and analytical achievements in organic matter research over the last two decades and demonstrate how these developments h...

Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling.

PubMed

Berthrong, Sean T; Buckley, Daniel H; Drinkwater, Laurie E

2013-07-01

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.

Drought causes substantial reductions in non-isothermal soil strength

NASA Astrophysics Data System (ADS)

Vahedifard, F.; Robinson, J. D.; Love, C. A.; AghaKouchak, A.

2016-12-01

The stability and settlement of natural slopes and engineering structures are governed primarily by the shear strength of foundation soil. Understanding soil-atmosphere interactions and their impacts on shear strength is imperative to evaluating drought impacts on the resilience of our infrastructure. This understanding is also important for assessing a variety of emerging science and engineering problems in a changing climate including analyzing existing and new infrastructures, landslides, soil carbon sequestration, land management, and managing traction and tillage in agriculture. While progress has been made in understanding shear strength response to soil moisture changes, the impacts of concurrent soil moisture and temperature changes on shear strength remain uncertain from a regional-scale perspective. Here we present a methodological framework based on various soil types, temperatures, and moistures, and surface fluxes, to quantify a non-isothermal soil shear strength. We employ a non-isothermal soil strength analysis (NISSA) to explore the extent to which elevated soil temperatures and low moistures, along with abnormal surface fluxes, during California's record-setting 2012 - 2015 drought reduced the soil's shear strength. Our results suggest that the prolonged California drought reduced the shear strength of fine-grained soil as much as 95%. In contrast, the NISSA suggests that drought impacts on coarse-grained soil were not as significant. These opposing behaviors are attributed to the existence and absence of intermolecular physico-chemical forces in fine- and coarse-grained soils, respectively. The outlined framework offers a unique avenue to explore how soil shear strength is likely to behave under extreme drought conditions.

Influence of Water Content on Pullout Behaviour of Geogrid

NASA Astrophysics Data System (ADS)

Chen, Rong; Song, Yang-yang; Hao, Dong-xue; Gao, Yu-cong

2017-06-01

The interaction between geogrid and soil is fundamental and crucial factor on safety and stability of geogrid-reinforced earth structure. Therefore, the interface index between geogrid and soil is of vital importance in the design of reinforced earth structures. The pullout behaviour of geogrid in soil is studied, an experimental investigation is conducted using geogrid in four groups of soil with 20%, 24%, 28%, 32% water contents, which correspond to normal stresses of 50, 100, 200 and 300 kPa respectively. The results indicate that the geogrid embedded in soil mainly represents pullout failure, and the ultimate pullout force is sensitive to water content. It decreases with the increase of the water content firstly. Besides, the water content influences the process of the pullout behaviour. The increase of water content leads to the ultimate pullout force soon.

Fluorescent antibody detection of microorganisms in terrestrial environments

NASA Technical Reports Server (NTRS)

Schmidt, E. L.

1972-01-01

The fluorescent antibody technique and its use in direct microscopic examination of the soil is discussed. Feasibility analyses were made to determine if the method could be used to simultaneously observe and recognize microorganisms in the soil. Some data indicate this may be possible. Data are also given on two related problems involving the interaction of soil microorganisms with plant roots to form symbiotic structures. One was concerned with the developmental ecology and biology of the root nodule of alder and the second was concerned with the ectotrophic mycorrhizal structure on forest trees, especially pines. In both, the fluorescent antibody detection of the microbial symbiont both as a free living form in soil, and as a root inhabiting form in the higher plant was emphasized. A third aspect of the research involved the detection of autotrophic ammonia oxidizing microorganisms in soil.

Ectomycorrhizal fungal associates of Pinus contorta in soils associated with a hot spring in Norris Geyser Basin, Yellowstone National Park, Wyoming

NASA Technical Reports Server (NTRS)

Cullings, K.; Makhija, S.

2001-01-01

Molecular methods and comparisons of fruiting patterns (i.e., presence or absence of fungal fruiting bodies in different soil types) were used to determine ectomycorrhizal (EM) associates of Pinus contorta in soils associated with a thermal soil classified as ultra-acidic to extremely acidic (pH 2 to 4). EM were sampled by obtaining 36 soil cores from six paired plots (three cores each) of both thermal soils and forest soils directly adjacent to the thermal area. Fruiting bodies (mushrooms) were collected for molecular identification and to compare fruiting body (above-ground) diversity to below-ground diversity. Our results indicate (i) that there were significant decreases in both the level of EM infection (130 +/- 22 EM root tips/core in forest soil; 68 +/- 22 EM root tips/core in thermal soil) and EM fungal species richness (4.0 +/- 0.5 species/core in forest soil; 1.2 +/- 0.2 species/core in thermal soil) in soils associated with the thermal feature; (ii) that the EM mycota of thermal soils was comprised of a small set of dominant species and included very few rare species, while the EM mycota of forest soils contained a few dominant species and several rare EM fungal species; (iii) that Dermocybe phoenecius and a species of Inocybe, which was rare in forest soils, were the dominant EM fungal species in thermal soils; (iv) that other than the single Inocybe species, there was no overlap in the EM fungal communities of the forest and thermal soils; and (v) that the fungal species forming the majority of the above-ground fruiting structures in thermal soils (Pisolithus tinctorius, which is commonly used in remediation of acid soils) was not detected on a single EM root tip in either type of soil. Thus, P. tinctorius may have a different role in these thermal soils. Our results suggest that this species may not perform well in remediation of all acid soils and that factors such as pH, soil temperature, and soil chemistry may interact to influence EM fungal community structure. In addition, we identified at least one new species with potential for use in remediation of hot acidic soil.

The Effects of Warming and Nitrogen Addition on Soil Nitrogen Cycling in a Temperate Grassland, Northeastern China

PubMed Central

Ma, Lin-Na; Lü, Xiao-Tao; Liu, Yang; Guo, Ji-Xun; Zhang, Nan-Yi; Yang, Jian-Qin; Wang, Ren-Zhong

2011-01-01

Background Both climate warming and atmospheric nitrogen (N) deposition are predicted to affect soil N cycling in terrestrial biomes over the next century. However, the interactive effects of warming and N deposition on soil N mineralization in temperate grasslands are poorly understood. Methodology/Principal Findings A field manipulation experiment was conducted to examine the effects of warming and N addition on soil N cycling in a temperate grassland of northeastern China from 2007 to 2009. Soil samples were incubated at a constant temperature and moisture, from samples collected in the field. The results showed that both warming and N addition significantly stimulated soil net N mineralization rate and net nitrification rate. Combined warming and N addition caused an interactive effect on N mineralization, which could be explained by the relative shift of soil microbial community structure because of fungal biomass increase and strong plant uptake of added N due to warming. Irrespective of strong intra- and inter-annual variations in soil N mineralization, the responses of N mineralization to warming and N addition did not change during the three growing seasons, suggesting independence of warming and N responses of N mineralization from precipitation variations in the temperate grassland. Conclusions/Significance Interactions between climate warming and N deposition on soil N cycling were significant. These findings will improve our understanding on the response of soil N cycling to the simultaneous climate change drivers in temperate grassland ecosystem. PMID:22096609

Influence of soil structure on nutrient cycling using microfluidic techniques

NASA Astrophysics Data System (ADS)

Arellano Caicedo, Carlos; Aleklett, Kristin; Ohlsson, Pelle; Hammer, Edith

2017-04-01

The rising of atmospheric CO2 levels and its effects on global warming make it necessary to understand the elements that regulate such levels and furthermore try to slow down the CO2 accumulation in the atmosphere. The exchange of carbon between soil and atmosphere plays a significant role in the atmospheric carbon budget. Soil organisms deposit organic compounds on and in soil aggregates, either as exudates or dead remains. Much of this dead organic material is quickly recycled, but a portion, however, will stay in the soil for long term. Evidence suggests that micro-scale biogeochemical interactions could play a highly significant role in degradation or persistence of organic matter in soils, thus, soil physical structure might play a decisive role in preventing accessibility of nutrients to microorganisms. For studying effects of spatial microstructure on soil nutrient cycles, we have constructed artificial habitats for microbes that simulate soil structures. Microfluidic, so called Lab-on-a-chip technologies, are one of the tools used to achieve our purpose. Such micro-habitats consist of pillar structures of difference density and surface area, tunnels with increasing depth, and mazes of increasing complexity to simulate different stages of soil aggregation. Using microscopy and analytical chemistry, we can follow the growth of microorganisms inoculated into the "soil chip" as well as the chemical degradation of organic matter compounds provided as nutrient source. In this way, we want to be able to predict how soil structure influences soil microbial activity leading to different effects on the carbon cycle. Our first results of a chip inoculated with natural soil showed a succession of organisms colonizing channels leading to dead-end arenas, starting with a high presence of bacteria inside the chip during the first days. Fungal hyphae growth gradually inside the channels until it finally occupied the big majority of the spaces isolating bacteria which dramatically decreased in number. The structure inside the soil chip changes dynamically due to the creation of biofilms. Such changes alter the spatial distribution inside the chip gradually, to the point of getting significantly different from the original structures. Fungal hyphae, bacterial biofilms, and microbial necro mass accumulation where the components altering the chip structure. These findings suggest that a considerable part of the soil structure is microbial biomass. Using Lab-on-a-chip techniques leads to the creation of a much more realistic soil and ecosystem model, resembling spatial and chemical complexity in real soil structures at a micrometer scale, the scale relevant for soil organisms. Understanding small-scale processes in the soils is crucial to predict carbon and nutrient cycling, and to enable us to give recommendations for soil management in agriculture, horticulture and nature conservation. If parameterization of soil structure as a central determinant for carbon sequestration is possible, it will allow strong argumentation for management practices that conserve and foster soil structure, such as low-tillage, support of mycorrhizal fungi, and reduction of heavy machinery usage.

Relationship between the erosion properties of soils and other parameters

USDA-ARS?s Scientific Manuscript database

Soil parameters are essential for erosion process prediction and ultimately improved model development, especially as they relate to dam and levee failure. Soil parameters including soil texture and structure, soil classification, soil compaction, moisture content, and degree of saturation can play...

Seismic response of elevated rectangular water tanks considering soil structure interaction

NASA Astrophysics Data System (ADS)

Visuvasam, J.; Simon, J.; Packiaraj, J. S.; Agarwal, R.; Goyal, L.; Dhingra, V.

2017-11-01

The overhead staged water tanks are susceptible for high lateral forces during earthquakes. Due to which, the failure of beam-columns joints, framing elements and toppling of tanks arise. To avoid such failures, they are analyzed and designed for lateral forced induced by devastating earthquakes assuming the base of the structures are fixed and considering functional needs, response reduction, soil types and severity of ground shaking. In this paper, the flexible base was provided as spring stiffness in order to consider the effect of soil properties on the seismic behaviour of water tanks. A linear time history earthquake analysis was performed using SAP2000. Parametric studies have been carried out based on various types of soils such as soft, medium and hard. The soil stiffness values highly influence the time period and base shear of the structure. The ratios of time period of flexible to fixed base and base shear of flexible to fixed base were observed against capacities of water tank and the overall height of the system. The both responses are found to be increased as the flexibility of soil medium decreases

Macroscopic and molecular approaches of enrofloxacin retention in soils in presence of Cu(II).

PubMed

Graouer-Bacart, Mareen; Sayen, Stéphanie; Guillon, Emmanuel

2013-10-15

The co-adsorption of copper and the fluoroquinolone antibiotic enrofloxacin (ENR) at the water-soil interface was studied by means of batch adsorption experiments, and extended X-ray absorption fine structure (EXAFS) spectroscopy. The system was investigated over a pH range between 6 and 10, at different contact times, ionic strengths, and ENR concentrations. Adsorption coefficient - Kd - was determined at relevant environmental concentrations and the value obtained in water at a ionic strength imposed by the soil and at soil natural pH was equal to 0.66Lg(-1). ENR adsorption onto the soil showed strong pH dependence illustrating the influence of the electrostatic interactions in the sorption processes. The simultaneous co-adsorption of ENR and Cu(II) on the soil was also investigated. The presence of Cu(II) strongly influenced the retention of the antibiotic, leading to an increase up to 35% of adsorbed ENR amount. The combined quantitative and spectroscopic results showed that Cu(II) and ENR directly interacted at the water-soil interface to form ternary surface complexes. Cu K-edge EXAFS data indicated a molecular structure where the carboxylate and carbonyl groups of ENR coordinate to Cu(II) to form a 6-membered chelate ring and where Cu(II) bridges between ENR and the soil surface sites. Cu(II) bonds bidentately to the surface in an inner-sphere mode. Thus, the spectroscopic data allowed us to propose the formation of ternary surface complexes with the molecular architecture soil-Cu(II)-ENR. Copyright © 2013 Elsevier Inc. All rights reserved.

Warming alters the energetic structure and function but not resilience of soil food webs

PubMed Central

Schwarz, Benjamin; Barnes, Andrew D.; Thakur, Madhav P.; Brose, Ulrich; Ciobanu, Marcel; Reich, Peter B.; Rich, Roy L.; Rosenbaum, Benjamin; Stefanski, Artur; Eisenhauer, Nico

2017-01-01

Climate warming is predicted to alter the structure, stability, and functioning of food webs1–5. Yet, despite the importance of soil food webs for energy and nutrient turnover in terrestrial ecosystems, warming effects on these food webs—particularly in combination with other global change drivers—are largely unknown. Here, we present results from two complementary field experiments testing the interactive effects of warming with forest canopy disturbance and drought on energy fluxes in boreal-temperate ecotonal forest soil food webs. The first experiment applied a simultaneous above- and belowground warming treatment (ambient, +1.7°C, +3.4°C) to closed canopy and recently clear-cut forest, simulating common forest disturbance6. The second experiment crossed warming with a summer drought treatment (-40% rainfall) in the clear-cut habitats. We show that warming reduces energy fluxes to microbes, while forest canopy disturbance and drought facilitates warming-induced increases in energy flux to higher trophic levels and exacerbates reductions in energy flux to microbes, respectively. Contrary to expectations, we find no change in whole-network resilience to perturbations, but significant losses of ecosystem functioning. Warming thus interacts with forest disturbance and drought, shaping the energetic structure of soil food webs and threatening the provisioning of multiple ecosystem functions in boreal-temperate ecotonal forests. PMID:29218059

Warming alters energetic structure and function but not resilience of soil food webs

NASA Astrophysics Data System (ADS)

Schwarz, Benjamin; Barnes, Andrew D.; Thakur, Madhav P.; Brose, Ulrich; Ciobanu, Marcel; Reich, Peter B.; Rich, Roy L.; Rosenbaum, Benjamin; Stefanski, Artur; Eisenhauer, Nico

2017-12-01

Climate warming is predicted to alter the structure, stability, and functioning of food webs1-5. Yet, despite the importance of soil food webs for energy and nutrient turnover in terrestrial ecosystems, the effects of warming on these food webs—particularly in combination with other global change drivers—are largely unknown. Here, we present results from two complementary field experiments that test the interactive effects of warming with forest canopy disturbance and drought on energy flux in boreal-temperate ecotonal forest soil food webs. The first experiment applied a simultaneous above- and belowground warming treatment (ambient, +1.7 °C, +3.4 °C) to closed-canopy and recently clear-cut forest, simulating common forest disturbance6. The second experiment crossed warming with a summer drought treatment (-40% rainfall) in the clear-cut habitats. We show that warming reduces energy flux to microbes, while forest canopy disturbance and drought facilitates warming-induced increases in energy flux to higher trophic levels and exacerbates the reduction in energy flux to microbes, respectively. Contrary to expectations, we find no change in whole-network resilience to perturbations, but significant losses in ecosystem functioning. Warming thus interacts with forest disturbance and drought, shaping the energetic structure of soil food webs and threatening the provisioning of multiple ecosystem functions in boreal-temperate ecotonal forests.

The effect of row structure on soil moisture retrieval accuracy from passive microwave data.

PubMed

Xingming, Zheng; Kai, Zhao; Yangyang, Li; Jianhua, Ren; Yanling, Ding

2014-01-01

Row structure causes the anisotropy of microwave brightness temperature (TB) of soil surface, and it also can affect soil moisture retrieval accuracy when its influence is ignored in the inversion model. To study the effect of typical row structure on the retrieved soil moisture and evaluate if there is a need to introduce this effect into the inversion model, two ground-based experiments were carried out in 2011. Based on the observed C-band TB, field soil and vegetation parameters, row structure rough surface assumption (Q p model and discrete model), including the effect of row structure, and flat rough surface assumption (Q p model), ignoring the effect of row structure, are used to model microwave TB of soil surface. Then, soil moisture can be retrieved, respectively, by minimizing the difference of the measured and modeled TB. The results show that soil moisture retrieval accuracy based on the row structure rough surface assumption is approximately 0.02 cm(3)/cm(3) better than the flat rough surface assumption for vegetated soil, as well as 0.015 cm(3)/cm(3) better for bare and wet soil. This result indicates that the effect of row structure cannot be ignored for accurately retrieving soil moisture of farmland surface when C-band is used.

Land application of tylosin and chlortetracycline swine manure: Impacts to soil nutrients and soil microbial community structure.

PubMed

Stone, James J; Dreis, Erin K; Lupo, Christopher D; Clay, Sharon A

2011-01-01

The land application of aged chortetracycle (CTC) and tylosin-containing swine manure was investigated to determine associated impacts to soil microbial respiration, nutrient (phosphorus, ammonium, nitrate) cycling, and soil microbial community structure under laboratory conditions. Two silty clay loam soils common to southeastern South Dakota were used. Aerobic soil respiration results using batch reactors containing a soil-manure mixture showed that interactions between soil, native soil microbial populations, and antimicrobials influenced CO(2) generation. The aged tylosin treatment resulted in the greatest degree of CO(2) inhibition, while the aged CTC treatment was similar to the no-antimicrobial treatment. For soil columns in which manure was applied at a one-time agronomic loading rate, there was no significant difference in soil-P behavior between either aged CTC or tylosin and the no-antimicrobial treatment. For soil-nitrogen (ammonium and nitrate), the aged CTC treatment resulted in rapid ammonium accumulation at the deeper 40cm soil column depth, while nitrate production was minimal. The aged CTC treatment microbial community structure was different than the no-antimicrobial treatment, where amines/amide and carbohydrate chemical guilds utilization profile were low. The aged tylosin treatment also resulted in ammonium accumulation at 40 cm column depth, however nitrate accumulation also occurred concurrently at 10 cm. The microbial community structure for the aged tylosin was also significantly different than the no-antimicrobial treatment, with a higher degree of amines/amides and carbohydrate chemical guild utilization compared to the no-antimicrobial treatment. Study results suggest that land application of CTC and tylosin-containing manure appears to fundamentally change microbial-mediated nitrogen behavior within soil A horizons.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

PubMed Central

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D.; Zhou, Jizhong

2015-01-01

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems. PMID:25791904

Impact of roots, mycorrhizas and earthworms on soil physical properties as assessed by shrinkage analysis

NASA Astrophysics Data System (ADS)

Milleret, R.; Le Bayon, R.-C.; Lamy, F.; Gobat, J.-M.; Boivin, P.

2009-07-01

SummarySoil biota such as earthworms, arbuscular mycorrhizal fungi (AMF) and plant roots are known to play a major role in engineering the belowground part of the terrestrial ecosystems, thus strongly influencing the water budget and quality on earth. However, the effect of soil organisms and their interactions on the numerous soil physical properties to be considered are still poorly understood. Shrinkage analysis allows quantifying a large spectrum of soil properties in a single experiment, with small standard errors. The objectives of the present study were, therefore, to assess the ability of the method to quantify changes in soil properties as induced by single or combined effects of leek roots ( Allium porrum), AMF ( Glomus intraradices) and earthworms ( Allolobophora chlorotica). The study was performed on homogenised soil microcosms and the experiments lasted 35 weeks. The volume of the root network and the external fungal hyphae was measured at the end, and undisturbed soil cores were collected. Shrinkage analysis allowed calculating the changes in soil hydro-structural stability, soil plasma and structural pore volumes, soil bulk density and plant available water, and structural pore size distributions. Data analysis revealed different impacts of the experimented soil biota on the soil physical properties. At any water content, the presence of A. chlorotica resulted in a decrease of the specific bulk volume and the hydro-structural stability around 25%, and in a significant increase in the bulk soil density. These changes went with a decrease of the structural pore volumes at any pore size, a disappearing of the thinnest structural pores, a decrease in plant available water, and a hardening of the plasma. On the contrary, leek roots decreased the bulk soil density up to 1.23 g cm -3 despite an initial bulk density of 1.15 g cm -3. This increase in volume was accompanied with a enhanced hydro-structural stability, a larger structural pore volume at any pore size, smaller structural pore radii and an increase in plant available water. Interestingly, a synergistic effect of leek roots and AMF in the absence of the earthworms was highlighted, and this synergistic effect was not observed in presence of earthworms. The structural pore volume generated by root and AMF growth was several orders of magnitude larger than the volume of the organisms. Root exudates as well as other AMF secretion have served as carbon source for bacteria that in turn would enhance soil aggregation and porosity, thus supporting the idea of a self-organization of the soil-plant-microbe complex previously described.

Soil ecosystem functioning under climate change: plant species and community effects.

PubMed

Kardol, Paul; Cregger, Melissa A; Campany, Courtney E; Classen, Aimee T

2010-03-01

Feedbacks of terrestrial ecosystems to atmospheric and climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering the soil communities that depend on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and precipitation in Tennessee (USA). Specifically, we collected soils at the plot level (plant community soils) and beneath dominant plant species (plant-specific soils). We used microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: (1) Overall, while there were some interactions, water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activity, and soil nematodes. Multiple climate-change factors can interact to shape ecosystems, but in our study, those interactions were largely driven by changes in water. (2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning, and this impact was not obvious when looking at plant community soils. Climate-change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. These results indicate that accurate assessments of climate-change impacts on soil ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate-change-induced shifts in plant community composition will likely modify or counteract the direct impact of atmospheric and climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting the manner in which global change will alter ecosystem functioning.

Interactions between fauna and environment in recent alluvial soils (Dunajec River, SE Poland)

NASA Astrophysics Data System (ADS)

Mikuś, Paweł; Uchman, Alfred

2017-04-01

Recent riverine system is a particular place for interactions between fauna and the deposited sediments containing young and old alluvial soils. It is characterized by large energy gradients in relatively short time, which forces special adaptations of burrowing animals recorded in bioturbation structures. Predators produce mainly shelter burrows (interpreted as domichnia), and saprofags, especially earthworms, produce locomotion and feeding structures (pascichnia). Such structures have been studied in non- or poorly vegetated, sandy or muddy Holocene alluvia in the lower reach of the Dunajec River flowing through the Carpathian Foredeep in SE Poland. The observed burrows are mostly produced by a variety of organisms, including the European mole (Talpa europaea), common earthworm (Lumbricus terrestris), ground beetles (Carabidae), solitary bees (Ammophila), red fox (Vulpes vulpes), European beaver (Castor fiber), shrews (Soricidae), European otter (Lutra lutra), several species of mice (Muridae), voles (Myodae, Microtae), and the swallow sand martin (Riparia riparia). Burrows of a few species of ground beetles have been subjected to more detailed studies. Fertile deposits of older (early to middle Holocene) terraces, formed with many long-term interruptions in sedimentation processes, have a well-developed soil levels, more vulnerable to burrowing than recently deposited sediments. The terraces contain layers of sands and muds, which primary sedimentary structures and layer boundaries are completely or partly disturbed by bioturbation. Organic-rich muds have been moved up and down and mixed with sand. Moreover, sediments have been leached into open burrows during floods or rainfalls. In the natural levee sediments, mostly fine to medium sands, are horizontally burrowed, foremost by earthworms (Lumbricidae). Vertical, long (over 2 m deep) burrows of larger earthworms cross cut the natural levee sediments and enter buried soils. They were formed during a long period between flooding events reaching into the soil profile. Not rarely, the vertical burrows follow living or dead roots. As the European mole feed on earthworms, their burrows commonly co-occur. Diversity and abundance of burrowing animals in the riverine environment are mainly controlled by water-level fluctuations, foremost these which cause floods or droughts. The highest biodiversity of infauna occurs under moderate level of river disturbances. With low level of disturbances, larger, long-living species dominate, whereas with high-level disturbances small, short-living forms prevail.

Interactions between soil thermal and hydrological dynamics in the response of Alaska ecosystems to fire disturbance

USGS Publications Warehouse

Yi, Shuhua; McGuire, A. David; Harden, Jennifer; Kasischke, Eric; Manies, Kristen L.; Hinzman, Larry; Liljedahl, Anna K.; Randerson, J.; Liu, Heping; Romanovsky, Vladimir E.; Marchenko, Sergey S.; Kim, Yongwon

2009-01-01

Soil temperature and moisture are important factors that control many ecosystem processes. However, interactions between soil thermal and hydrological processes are not adequately understood in cold regions, where the frozen soil, fire disturbance, and soil drainage play important roles in controlling interactions among these processes. These interactions were investigated with a new ecosystem model framework, the dynamic organic soil version of the Terrestrial Ecosystem Model, that incorporates an efficient and stable numerical scheme for simulating soil thermal and hydrological dynamics within soil profiles that contain a live moss horizon, fibrous and amorphous organic horizons, and mineral soil horizons. The performance of the model was evaluated for a tundra burn site that had both preburn and postburn measurements, two black spruce fire chronosequences (representing space-for-time substitutions in well and intermediately drained conditions), and a poorly drained black spruce site. Although space-for-time substitutions present challenges in model-data comparison, the model demonstrates substantial ability in simulating the dynamics of evapotranspiration, soil temperature, active layer depth, soil moisture, and water table depth in response to both climate variability and fire disturbance. Several differences between model simulations and field measurements identified key challenges for evaluating/improving model performance that include (1) proper representation of discrepancies between air temperature and ground surface temperature; (2) minimization of precipitation biases in the driving data sets; (3) improvement of the measurement accuracy of soil moisture in surface organic horizons; and (4) proper specification of organic horizon depth/properties, and soil thermal conductivity.

Press-pulse interactions: effects of warming, N deposition, altered winter precipitation, and fire on desert grassland community structure and dynamics.

PubMed

Collins, Scott L; Ladwig, Laura M; Petrie, Matthew D; Jones, Sydney K; Mulhouse, John M; Thibault, James R; Pockman, William T

2017-03-01

Global environmental change is altering temperature, precipitation patterns, resource availability, and disturbance regimes. Theory predicts that ecological presses will interact with pulse events to alter ecosystem structure and function. In 2006, we established a long-term, multifactor global change experiment to determine the interactive effects of nighttime warming, increased atmospheric nitrogen (N) deposition, and increased winter precipitation on plant community structure and aboveground net primary production (ANPP) in a northern Chihuahuan Desert grassland. In 2009, a lightning-caused wildfire burned through the experiment. Here, we report on the interactive effects of these global change drivers on pre- and postfire grassland community structure and ANPP. Our nighttime warming treatment increased winter nighttime air temperatures by an average of 1.1 °C and summer nighttime air temperature by 1.5 °C. Soil N availability was 2.5 times higher in fertilized compared with control plots. Average soil volumetric water content (VWC) in winter was slightly but significantly higher (13.0% vs. 11.0%) in plots receiving added winter rain relative to controls, and VWC was slightly higher in warmed (14.5%) compared with control (13.5%) plots during the growing season even though surface soil temperatures were significantly higher in warmed plots. Despite these significant treatment effects, ANPP and plant community structure were highly resistant to these global change drivers prior to the fire. Burning reduced the cover of the dominant grasses by more than 75%. Following the fire, forb species richness and biomass increased significantly, particularly in warmed, fertilized plots that received additional winter precipitation. Thus, although unburned grassland showed little initial response to multiple ecological presses, our results demonstrate how a single pulse disturbance can interact with chronic alterations in resource availability to increase ecosystem sensitivity to multiple drivers of global environmental change. © 2016 John Wiley & Sons Ltd.

Geotechnical centrifuge use at University of Cambridge Geotechnical Centre, August-September 1991

NASA Astrophysics Data System (ADS)

Gilbert, Paul A.

1992-01-01

A geotechnical centrifuge applies elevated acceleration to small-scale soil models to simulate body forces and stress levels characteristic of full-size soil structures. Since the constitutive behavior of soil is stress level development, the centrifuge offers considerable advantage in studying soil structures using models. Several experiments were observed and described in relative detail, including experiments in soil dynamics and liquefaction study, an experiment investigation leaning towers on soft foundations, and an experiment investigating migration of hot pollutants through soils.

Development of in-structure design spectra for dome mounted equipment on underground waste storage tanks at the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Julyk, L.J.

1995-09-01

In-structure response spectra for dome mounted equipment on underground waste storage tanks at the Hanford Site are developed on the basis of recent soil-structure-interaction analyses. Recommended design spectra are provided for various locations on the tank dome.

Soil solution dynamics of Cu and Zn in a Cu- and Zn-polluted soil as influenced by gamma-irradiation and Cu-Zn interaction.

PubMed

Luo, Y M; Yan, W D; Christie, P

2001-01-01

A pot experiment was conducted to study soil solution dynamics of Cu and Zn in a Cu/Zn-polluted soil as influenced by gamma-irradiation and Cu-Zn interaction. A slightly acid sandy loam was amended with Cu and Zn (as nitrates) either singly or in combination (100 mg Cu and 150 mg Zn kg(-1) soil) and was then gamma-irradiated (10 kGy). Unamended and unirradiated controls were included, and spring barley (Hordeum vulgare L. cv. Forrester) was grown for 50 days. Soil solution samples obtained using soil moisture samplers immediately before transplantation and every ten days thereafter were used directly for determination of Cu, Zn, pH and absorbance at 360 nm (A360). Cu and Zn concentrations in the solution of metal-polluted soil changed with time and were affected by gamma-irradiation and metal interaction. gamma-Irradiation raised soil solution Cu substantially but generally decreased soil solution Zn. These trends were consistent with increased dissolved organic matter (A360) and solution pH after gamma-irradiation. Combined addition of Cu and Zn usually gave higher soil solution concentrations of Cu or Zn compared with single addition of Cu or Zn in gamma-irradiated and non-irradiated soils, indicating an interaction between Cu and Zn. Cu would have been organically complexed and consequently maintained a relatively high concentration in the soil solution under higher pH conditions. Zn tends to occur mainly as free ion forms in the soil solution and is therefore sensitive to changes in pH. The extent to which gamma-irradiation and metal interaction affected solubility and bioavailability of Cu and Zn was a function of time during plant growth. Studies on soil solution metal dynamics provide very useful information for understanding metal mobility and bioavailability.

Soil ecosystem functioning under climate change: plant species and community effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kardol, Paul; Cregger, Melissa; Campany, Courtney E

2010-01-01

Feedbacks of terrestrial ecosystems to climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering the microbial communities that feed on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and water availability. Specifically, we collected soils at the plot level (plant community soils), and beneathmore » dominant plant species (plant-specific soils). We used microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: 1) Overall, while there were some interactions, water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activities, and soil nematodes. Multiple climate change factors can interact to shape ecosystems, but in this case, those interactions were largely driven by changes in water availability. 2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning and this impact was not obvious when looking at plant community soils. Climate change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. In sum, these results indicate that accurate assessments of climate change impacts on soil ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate change-induced shifts in plant community composition will likely modify or counteract the direct impact of climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting how climate change will alter ecosystem functioning.« less

Development of a Coupled Framework for Simulating Interactive Effects of Frozen Soil Hydrological Dynamics in Permafrost Regions

DTIC Science & Technology

2013-11-01

Permafrost Input Database Geology, Lithologic Data, Snow Cover, Air Temperature, Ground Temperatures, Vegetation Precipitation Soil Properties GIPL...be found in Nicolsky et al. (2007). Required input data include climate data, snow cover, soil thermal properties, lithological data, and vegetative

Will nitrogen deposition mitigate warming-increased soil respiration in a young subtropical plantation?

Treesearch

Xiaofei Liu; Zhijie Yang; Chengfang Lin; Christian P. Giardina; Decheng Xiong; Weisheng Lin; Shidong Chen; Chao Xu; Guangshui Chen; Jinsheng Xie; Yiqing Li; Yusheng Yang

2017-01-01

Global change such as climate warming and nitrogen (N) deposition is likely to alter terrestrial carbon (C) cycling, including soil respiration (Rs), the largest CO2 source from soils to the atmosphere. To examine the effects of warming, N addition and their interactions on Rs, we...

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes.

PubMed

Hu, Hang-Wei; Wang, Jun-Tao; Singh, Brajesh K; Liu, Yu-Rong; Chen, Yong-Liang; Zhang, Yu-Jing; He, Ji-Zheng

2018-04-24

Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities.

PubMed

Rojas, Xavier; Guo, Jingqi; Leff, Jonathan W; McNear, David H; Fierer, Noah; McCulley, Rebecca L

2016-07-01

Tall fescue (Schedonorus arundinaceus) is a widespread grass that can form a symbiotic relationship with a shoot-specific fungal endophyte (Epichloë coenophiala). While the effects of fungal endophyte infection on fescue physiology and ecology have been relatively well studied, less attention has been given to how this relationship may impact the soil microbial community. We used high-throughput DNA sequencing and phospholipid fatty acid analysis to determine the structure and biomass of microbial communities in both bulk and rhizosphere soils from tall fescue stands that were either uninfected with E. coenophiala or were infected with the common toxic strain or one of several novel strains of the endophyte. We found that rhizosphere and bulk soils harbored distinct microbial communities. Endophyte presence, regardless of strain, significantly influenced soil fungal communities, but endophyte effects were less pronounced in prokaryotic communities. E. coenophiala presence did not change total fungal biomass but caused a shift in soil and rhizosphere fungal community composition, increasing the relative abundance of taxa within the Glomeromycota phylum and decreasing the relative abundance of genera in the Ascomycota phylum, including Lecanicillium, Volutella, Lipomyces, Pochonia, and Rhizoctonia. Our data suggests that tripartite interactions exist between the shoot endophyte E. coenophiala, tall fescue, and soil fungi that may have important implications for the functioning of soils, such as carbon storage, in fescue-dominated grasslands.

Metagenomic Insights of Microbial Feedbacks to Elevated CO2 (Invited)

NASA Astrophysics Data System (ADS)

Zhou, J.; Tu, Q.; Wu, L.; He, Z.; Deng, Y.; Van Nostrand, J. D.

2013-12-01

Understanding the responses of biological communities to elevated CO2 (eCO2) is a central issue in ecology and global change biology, but its impacts on the diversity, composition, structure, function, interactions and dynamics of soil microbial communities remain elusive. In this study, we first examined microbial responses to eCO2 among six FACE sites/ecosystems using a comprehensive functional gene microarray (GeoChip), and then focused on details of metagenome sequencing analysis in one particular site. GeoChip is a comprehensive functional gene array for examining the relationships between microbial community structure and ecosystem functioning and is a very powerful technology for biogeochemical, ecological and environmental studies. The current version of GeoChip (GeoChip 5.0) contains approximately 162,000 probes from 378,000 genes involved in C, N, S and P cycling, organic contaminant degradation, metal resistance, antibiotic resistance, stress responses, metal homeostasis, virulence, pigment production, bacterial phage-mediated lysis, soil beneficial microorganisms, and specific probes for viruses, protists, and fungi. Our experimental results revealed that both ecosystem and CO2 significantly (p < 0.05) affected the functional composition, structure and metabolic potential of soil microbial communities with the ecosystem having much greater influence (~47%) than CO2 (~1.3%) or CO2 and ecosystem (~4.1%). On one hand, microbial responses to eCO2 shared some common patterns among different ecosystems, such as increased abundances for key functional genes involved in nitrogen fixation, carbon fixation and degradation, and denitrification. On the other hand, more ecosystem-specific microbial responses were identified in each individual ecosystem. Such changes in the soil microbial community structure were closely correlated with geographic distance, soil NO3-N, NH4-N and C/N ratio. Further metagenome sequencing analysis of soil microbial communities in one particular site showed eCO2 altered the overall structure of soil microbial communities with ambient CO2 samples retaining a higher functional gene diversity than eCO2 samples. Also the taxonomic diversity of functional genes decreased at eCO2. Random matrix theory (RMT)-based network analysis showed that the identified networks under ambient and elevated CO2 were substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher order organization (meta-modules), topological roles of individual nodes, and network hubs, indicating that elevated CO2 dramatically altered the network interactions among different phylogenetic and functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen content, indicating the potential importance of network interactions in ecosystem functioning. Taken together, this study indicates that eCO2 may decrease the overall functional and taxonomic diversity of soil microbial communities, but such effects appeared to be ecosystem-specific, which makes it more challenging for predicting global or regional terrestrial ecosystems responses to eCO2.

Soil mechanics results of Luna 16 and Lunokhod 1: A preliminary report

NASA Technical Reports Server (NTRS)

Johnson, S. W.; Carrier, W. D., III

1971-01-01

The physical and mechanical properties of the lunar soil, as determined by Luna 16 and Lunokhod 1 experiments, are discussed. Data are included for interactions between vehicle wheels and the lunar soil, compressibility, resistance to penetration, and friction characteristics of the soil. The shear strength of the returned lunar soil for various bulk densities is also examined. Several potential spacecraft materials were tested in contact with lunar soil to determine their friction and wear characteristics.

Soil communities and plant litter decomposition as influenced by forest debris: Variation across tropical riparian and upland sites.

Treesearch

Honghua Ruana; Yiqing Lib; Xiaoming Zouc

2005-01-01

Forest debris on ground surface can interact with soil biota and consequently change ecosystem processes across heterogeneous landscape. We examined the interactions between forest debris and litter decomposition in riparian and upland sites within a tropical wet forest. Our experiment included control and debris-removal treatments. Debris-removal reduced leaf litter...

The effects of vegetation cover on soil nematode communities in various biotopes disturbed by industrial emissions.

PubMed

Šalamún, Peter; Hanzelová, Vladimíra; Miklisová, Dana; Šestinová, Oľga; Findoráková, Lenka; Kováčik, Peter

2017-08-15

Better understanding of interactions among belowground and aboveground components in biotopes may improve our knowledge about soil ecosystem, and is necessary in environment assessment using indigenous soil organisms. In this study, we proposed that in disturbed biotopes, vegetation play important role in the buffering of contamination impact on soil communities and decrease the ecological pressure on soil biota. To assess the effects of these interactions we compared nematode communities, known for their bioindication abilities, from four types of disturbed and undisturbed biotopes (coniferous forest, permanent grassland, agricultural field, clearings), where the main stress agent was represented by long-term acidic industrial emissions containing heavy metals (As, Cd, Cu, and Pb). To understand the ecological interactions taking place in studied biotopes, we studied abiotic factors (soil properties) and biotic factors (vegetation, nematode communities). Except significant increase in metals total and mobile concentrations in disturbed biotopes soil, we found acidification of soil horizon, mainly in the clearings (pH=3.68), due to SO 2 precipitation. These factors has caused in clearings degradation of native phytocoenoses and decrease in decomposition rate characterized by high amount of organic matter (C ox =4.29%). Nematodes reacts to these conditions by shifts in trophic structure (bacteriovores to fungal feeders), increase in c-p 2 genera (Aphelenchoides, Acrobeloides, and Cephalobus), absence of sensitive groups (c-p 3-5, omnivores, predators), and decrease in ecological indices (SI, MI, MI2-5, H'). Similar contamination was found in forest biotope, but the nematodes composition indicates more suitable conditions; more complex community structure (presence of sensitive trophic and higher c-p groups), higher abundance and indices values, comparable with less stressed field and grassland biotopes. As showed our results, the vegetation undoubtedly plays an important role not only as a resource of services indispensable for the ecosystem, but also as a significant buffer of negative impacts acting within. Copyright © 2017 Elsevier B.V. All rights reserved.

Interaction of brassicaceous seed meal and apple rootstock on recovery of Pythium spp. and Pratylenchus penetrans from roots grown in replant soils

USDA-ARS?s Scientific Manuscript database

Pythium spp. and Pratylenchus penetrans are significant components of the diverse pathogen complex that incites apple replant disease in Washington state. The structure of the Pythium population differs among orchard soils but is composed of multiple pathogenic species. Studies were conducted to d...

Evidence for the functional significance of diazotroph community structure in soil.

PubMed

Hsu, Shi-Fang; Buckley, Daniel H

2009-01-01

Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.

Modelling the Impact of Soil Management on Soil Functions

NASA Astrophysics Data System (ADS)

Vogel, H. J.; Weller, U.; Rabot, E.; Stößel, B.; Lang, B.; Wiesmeier, M.; Urbanski, L.; Wollschläger, U.

2017-12-01

Due to an increasing soil loss and an increasing demand for food and energy there is an enormous pressure on soils as the central resource for agricultural production. Besides the importance of soils for biomass production there are other essential soil functions, i.e. filter and buffer for water, carbon sequestration, provision and recycling of nutrients, and habitat for biological activity. All these functions have a direct feed back to biogeochemical cycles and climate. To render agricultural production efficient and sustainable we need to develop model tools that are capable to predict quantitatively the impact of a multitude of management measures on these soil functions. These functions are considered as emergent properties produced by soils as complex systems. The major challenge is to handle the multitude of physical, chemical and biological processes interacting in a non-linear manner. A large number of validated models for specific soil processes are available. However, it is not possible to simulate soil functions by coupling all the relevant processes at the detailed (i.e. molecular) level where they are well understood. A new systems perspective is required to evaluate the ensemble of soil functions and their sensitivity to external forcing. Another challenge is that soils are spatially heterogeneous systems by nature. Soil processes are highly dependent on the local soil properties and, hence, any model to predict soil functions needs to account for the site-specific conditions. For upscaling towards regional scales the spatial distribution of functional soil types need to be taken into account. We propose a new systemic model approach based on a thorough analysis of the interactions between physical, chemical and biological processes considering their site-specific characteristics. It is demonstrated for the example of soil compaction and the recovery of soil structure, water capacity and carbon stocks as a result of plant growth and biological activity. Coupling of the observed nonlinear interactions allows for modeling the stability and resilience of soil systems in terms of their essential functions.

Plant assemblage composition and soil P concentration differentially affect communities of AM and total fungi in a semi-arid grassland.

PubMed

Klabi, Rim; Bell, Terrence H; Hamel, Chantal; Iwaasa, Alan; Schellenberg, Mike; Raies, Aly; St-Arnaud, Marc

2015-01-01

Adding inorganic P- and N-fixing legumes to semi-arid grasslands can increase forage yield, but soil nutrient concentrations and plant cover may also interact to modify soil fungal populations, impacting short- and long-term forage production. We tested the effect of plant assemblage (seven native grasses, seven native grasses + the domesticated N-fixing legume Medicago sativa, seven native grasses + the native N-fixing legume Dalea purpurea or the introduced grass Bromus biebersteinii + M. sativa) and soil P concentration (addition of 0 or 200 P2O5 kg ha(-1) at sowing) on the diversity and community structure of arbuscular mycorrhizal (AM) fungi and total fungi over two consecutive years, using 454-pyrosequencing of 18S rDNA and ITS amplicons. Treatment effects were stronger in the wet year (2008) than the dry year (2009). The presence of an N-fixing legume with native grasses generally increased AM fungal diversity, while the interaction between soil P concentration and plant assemblage modified total fungal community structure in 2008. Excluding interannual variations, which are likely driven by moisture and plant productivity, AM fungal communities in semi-arid grasslands appear to be primarily affected by plant assemblage composition, while the composition of other fungi is more closely linked to soil P. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Functional Plant Types Drive Plant Interactions in a Mediterranean Mountain Range

PubMed Central

Macek, Petr; Prieto, Iván; Macková, Jana; Pistón, Nuria; Pugnaire, Francisco I.

2016-01-01

Shrubs have positive (facilitation) and negative (competition) effects on understory plants, the net interaction effect being modulated by abiotic conditions. Overall shrubs influence to great extent the structure of plant communities where they have significant presence. Interactions in a plant community are quite diverse but little is known about their variability and effects at community level. Here we checked the effects of co-occurring shrub species from different functional types on a focal understory species, determining mechanisms driving interaction outcome, and tested whether effects measured on the focal species were a proxy for effects measured at the community level. Growth, physiological, and reproductive traits of Euphorbia nicaeensis, our focal species, were recorded on individuals growing in association with four dominant shrub species and in adjacent open areas. We also recorded community composition and environmental conditions in each microhabitat. Shrubs provided environmental conditions for plant growth, which contrasted with open areas, including moister soil, greater N content, higher air temperatures, and lower radiation. Shrub-associated individuals showed lower reproductive effort and greater allocation to growth, while most physiological traits remained unaffected. Euphorbia individuals were bigger and had more leaf N under N-fixing than under non-fixing species. Soil moisture was also higher under N-fixing shrubs; therefore soil conditions in the understory may counter reduced light conditions. There was a significant effect of species identity and functional types in the outcome of plant interactions with consistent effects at individual and community levels. The contrasting allocation strategies to reproduction and growth in Euphorbia plants, either associated or not with shrubs, showed high phenotypic plasticity and evidence its ability to cope with contrasting environmental conditions. PMID:27242863

Functional Plant Types Drive Plant Interactions in a Mediterranean Mountain Range.

PubMed

Macek, Petr; Prieto, Iván; Macková, Jana; Pistón, Nuria; Pugnaire, Francisco I

2016-01-01

Shrubs have positive (facilitation) and negative (competition) effects on understory plants, the net interaction effect being modulated by abiotic conditions. Overall shrubs influence to great extent the structure of plant communities where they have significant presence. Interactions in a plant community are quite diverse but little is known about their variability and effects at community level. Here we checked the effects of co-occurring shrub species from different functional types on a focal understory species, determining mechanisms driving interaction outcome, and tested whether effects measured on the focal species were a proxy for effects measured at the community level. Growth, physiological, and reproductive traits of Euphorbia nicaeensis, our focal species, were recorded on individuals growing in association with four dominant shrub species and in adjacent open areas. We also recorded community composition and environmental conditions in each microhabitat. Shrubs provided environmental conditions for plant growth, which contrasted with open areas, including moister soil, greater N content, higher air temperatures, and lower radiation. Shrub-associated individuals showed lower reproductive effort and greater allocation to growth, while most physiological traits remained unaffected. Euphorbia individuals were bigger and had more leaf N under N-fixing than under non-fixing species. Soil moisture was also higher under N-fixing shrubs; therefore soil conditions in the understory may counter reduced light conditions. There was a significant effect of species identity and functional types in the outcome of plant interactions with consistent effects at individual and community levels. The contrasting allocation strategies to reproduction and growth in Euphorbia plants, either associated or not with shrubs, showed high phenotypic plasticity and evidence its ability to cope with contrasting environmental conditions.

International Critical Zone Science: Opportunities to Build a Global Understanding of Land-Water Linkages

NASA Astrophysics Data System (ADS)

McDowell, W. H.

2015-12-01

Critical Zone science examines the structure and properties of the thin veneer that links surface properties to deep geology, at time scales of seconds to millennia. One of the fundamental premises of the US Critical Zone Observatories program is that CZOs should include some measurements made in common at all sites, as these common measurements will enable us to make stronger inferences about how the structure and function of the critical zone interact to drive key processes such as soil formation, stream flow generation, and nutrient export. Recent advances in real-time sensors provide new opportunities to address some fundamental questions about how hillslope soils and streams are linked. Data from the Luquillo Critical Zone Observatory in Puerto Rico, for example, document a previously undescribed transition, or flipping, of stream and soil biogeochemistry in a tropical rain forest. Under typical conditions, soil moisture is high and soil oxygen content is often low, especially at depth. Streams, in contrast, are typically near oxygen saturation. Under severe drought, however, oxygen increases dramatically in soil air and declines to values that are well below saturation in streams. This flipping in redox conditions suggests that despite the strong hydrologic connection between hillslope and stream, gas dynamics and potentially solute dynamics are decoupled along the flow path. The international CZO community has the opportunity to develop a suite of sensor arrays to document soil air, groundwater chemistry, and stream water chemistry. Progress towards realizing the potential of these international networks to develop coherent sensor programs will be addressed based on the current status of sensor deployments in CZO networks in the US, China, and Europe.

Use of planetary soils within CELSS: The plant viewpoint

NASA Astrophysics Data System (ADS)

Art Spomer, L.

1994-11-01

The major functions of soil relative to plant growth include retention and supply of water and minerals, provision of anchorage and support for the root, and provision of an otherwise adequate physical and chemical environment to ensure an extensive, functioning root system. The physical and chemical nature of the solid matrix constituting a soil interacts with the soil confinement configuration, the growing environment, and plant requirements to determine the soil's suitability for plant growth. A wide range of natural and manufactured terrestrial materials have proven adequate soils provided they are not chemically harmful to plants (or animals eating the plants), are suitably prepared for the specific use, and are used in a compatible confinement system. It is presumed this same rationale can be applied to planetary soils for growing plants within any controlled environment life support system (CELSS). The basic concepts of soil and soil-plant interactions are reviewed relative to using soils constituted from local planetary materials for growing plants.

Acid rain and its ecological consequences.

PubMed

Singh, Anita; Agrawal, Madhoolika

2008-01-01

Acidification of rain-water is identified as one of the most serious environmental problems of transboundary nature. Acid rain is mainly a mixture of sulphuric and nitric acids depending upon the relative quantities of oxides of sulphur and nitrogen emissions. Due to the interaction of these acids with other constituents of the atmosphere, protons are released causing increase in the soil acidity Lowering of soil pH mobilizes and leaches away nutrient cations and increases availability of toxic heavy metals. Such changes in the soil chemical characteristics reduce the soil fertility which ultimately causes the negative impact on growth and productivity of forest trees and crop plants. Acidification of water bodies causes large scale negative impact on aquatic organisms including fishes. Acidification has some indirect effects on human health also. Acid rain affects each and every components of ecosystem. Acid rain also damages man-made materials and structures. By reducing the emission of the precursors of acid rain and to some extent by liming, the problem of acidification of terrestrial and aquatic ecosystem has been reduced during last two decades.

MASTODON: A geosciences simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture (extended finite-element method), and porous media, among others. The tensor mechanics and contact modules, in particular, are well suited for nonlinear geosciences problems. Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON; https://seismic-research.inl.gov/SitePages/Mastodon.aspx)--a MOOSE-based application--is capable of analyzing the response of 3D soil-structure systems to external hazards with current development focused on earthquakes. It is capable of simulating seismic events and can perform extensive "source-to-site" simulations including earthquake fault rupture, nonlinear wave propagation, and nonlinear soil-structure interaction analysis. MASTODON also includes a dynamic probabilistic risk assessment capability that enables analysts to not only perform deterministic analyses, but also easily perform probabilistic or stochastic simulations for the purpose of risk assessment. Although MASTODON has been developed for the nuclear industry, it can be used to assess the risk for any structure subjected to earthquakes.The geosciences community can learn from the nuclear industry and harness the enormous effort underway to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The geosciences community could benefit from existing tools by enabling collaboration between researchers and practitioners throughout the world and advance the state-of-the-art in line with other scientific research efforts.

Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hofmockel, Kirsten; Hobbie, Erik

Our funded research focused on soil organic matter dynamics and plant-microbe interactions by examining the role of belowground processes and mechanisms across scales, including decomposition of organic molecules, microbial interactions, and plant-microbe interactions associated with a changing climate. Research foci included mycorrhizal mediated priming of soil carbon turnover, organic N use and depolymerization by free-living microbes and mycorrhizal fungi, and the use of isotopes as additional constraints for improved modeling of belowground processes. This work complemented the DOE’s mandate to understand both the consequences of atmospheric and climatic change for key ecosystems and the feedbacks on C cycling.

Soil humic substances hinder the propagation of prions

NASA Astrophysics Data System (ADS)

Leita, Liviana; Giachin, Gabriele; Margon, Alja; Narkiewicz, Joanna; Legname, Giuseppe

2013-04-01

Prions are infectious pathogens causing fatal neurodegenerative disorders, known as transmissible spongiform encephalopathies (TSEs), or prion diseases, which affect different mammalian species. TSEs include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) in mule deer, elk, and moose (cervids), and Creutzfeldt-Jakob disease (CJD) in humans. The prominent, if not only, component of prions is a misfolded conformer (PrPSc) of a constitutive sialoglycoprotein, the cellular prion protein (PrPC). A notable feature of prion diseases is horizontal transmission between grazing animals, implying that contaminated soil may serve to propagate the disease. In this respect, it has been reported that grazing animals ingest from tens to hundreds grams of soil per day, either incidentally through the diet, or deliberately in answering salt needs, and that mule deer can develop CWD after grazing in locations that previously housed infected animals. Prions may enter the environment through different routes, including animal excreta and secreta which mainly contribute to soil contamination. Recent studies have proven that prions can be retained in soil, which could act as a carrier of infectivity even several years after the contamination. However, within the large spread of potentially infected lands, prion diseases have become endemic only in geographically limited regions. The reasons for this geographical distribution remain unknown, but it suggests a role of the different kinds of soil in either enhancing or attenuating prion infectivity. The extent of prion transmission from the contaminated environment is unknown. Several studies have tried to address the issue of prion interaction with soil, but, at the present, different approaches show several drawbacks and technical difficulties, as soil is a complex, multi-component system of both mineral and organic interacting substances. Most research has focused on the adsorption capacity of clay minerals; however the contribution of soil organic components in adsorption has so far been neglected, as they represent a minor soil fraction on a weight basis. Among organic molecules, humic substances (HSs) are natural polyanions that result among the most reactive compounds in the soil and possess the largest specific surface area. Humic substances make up a large portion of the dark matter in humus and consist of heterogeneous mixtures of transformed biomolecules exhibiting a supramolecular structure. HSs are classified as humic acids (HAs), which are soluble only in alkaline solutions, and fulvic acids (FAs), which are soluble in both alkaline and acid solutions. The amphiphilic characteristics confer to HAs and FAs great versatility to interact with xenobiotics and reasonably also with prion proteins and/or prions too, leading to the formation of adducts with peculiar chemical and biophysical characteristics, thus affecting the transport, fixation and toxicity of prion. Results from our chemical, biophysical and biochemical investigation will be presented and results on anti-prion activity exerted by HAs and FAs will be provided, thus suggesting that amendment of contaminated soil with humic substances could be a strategy to contrast prion diffusion.

Geohazards: Natural and man-made

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCall, G.J.H.; Laming, D.J.C.; Scott, S.C.

1992-01-01

This book of conference presentations from a meeting of the Geological Society of London in 1989 includes 20 papers grouped in 5 sections. Sections include the following: volcanos; earthquakes; landslides; quiet hazards such as sea-level changes and loss of soils or biodiversity; discussion of the question of what can be done to reduce such disasters. Interaction of man's activities to initiate disasters, to increase the scope of disasters and/or to mitigate them is included in a number of papers. In the fourth section a final paper provides a summary of the food-soil, energy-climate, waste-garbage, and water-contamination interactions.

Mobilization of interactions between functional diversity of plant and soil organisms on nitrogen availability and use

NASA Astrophysics Data System (ADS)

Drut, Baptiste; Cassagne, Nathalie; Cannavacciuolo, Mario; Brauman, Alain; Le Floch, Gaëtan; Cobo, Jose; Fustec, Joëlle

2017-04-01

Keywords: legumes, earthworms, microorganisms, nitrogen, interactions Both aboveground and belowground biodiversity and their interactions can play an important role in crop productivity. Plant functional diversity, such as legume based intercrops have been shown to improve yields through plant complementarity for nitrogen use (Corre-Hellou et al., 2006). Moreover, plant species or plant genotype may influence the structure of soil microorganism communities through the composition of rhizodeposits in the rhizosphere (Dennis et al., 2010). Belowground diversity can also positively influence plant performance especially related to functional dissimilarity between soil organisms (Eisenhauer, 2012). Earthworms through their burrowing activity influence soil microbial decomposers and nutrient availability and have thus been reported to increase plant growth (Brown, 1995; Brown et al., 2004). We hypothesize that i) plant functional (genetic and/or specific) diversity associated to functional earthworms diversity are key drivers of interactions balance to improve crop performances and ii) the improvement of plant performances can be related to change in the structure of soil microorganism communities due to the diversity of rhizodeposits and the burrowing activity of earthworms. In a first mesocosm experiment, we investigated the effect of a gradient of plant diversity - one cultivar of wheat (Triticum aestivum L.), 3 different wheat cultivars, and 3 different cultivars intercropped with clover (Trifolium hybridum L.) - and the presence of one (endogeic) or two (endogeic and anecic) categories of earthworms on biomass and nitrogen accumulation of wheat. In a second mesocosm experiment, we investigated the influence of three species with different rhizodeposition - wheat, rapeseed (Brassica napus L. ) and faba bean (Vicia faba L.) in pure stand or intercropped - and the presence of endogeic earthworms on microbial activity and nitrogen availability. In the first experiment, biomass and nitrogen accumulation of wheat were improved in the presence of earthworms and clover. No effect of a plant genetic diversity was shown on crop performances. Furthermore, the influence of earthworms on bacterial diversity depended on plant diversity. In the second experiment, the specific composition of plant and earthworm presence modified the physiological profiles of rhizospheric microorganism communities (Microresp®) and nitrification potential. In the presence of faba-bean, microorganism activity was consistently increased and earthworms tended to decrease C:N ratio in the rhizospheric soil. These results confirm the interest of legume based intercrops for the complementarity in nitrogen use thanks to biological fixation. This study showed the influence of earthworms on plant nitrogen acquisition by stimulating microorganism activity and nutrient availability around the roots. We also highlighted a synergistic effect between the presence of legume and endogeic earthworms for higher plant performances. We finally hypothesized that the combined effect of rhizodeposit diversity related to plant specific composition and soil chemical properties modified by earthworm activity drives the structure and activity of microorganism communities. Brown, G.G., 1995. How do earthworms affect microfloral and faunal community diversity? Plant and Soil 170, 209-231. Brown, G.G., Edwards, C.A., Brussaard, L., 2004. How earthworms affect plant growth: burrowing into the mechanisms. Earthworm ecology 2, 13-49. Corre-Hellou, G., Fustec, J., Crozat, Y., 2006. Interspecific competition for soil N and its interaction with N2 fixation, leaf expansion and crop growth in pea-barley intercrops. Plant and Soil 282, 195-208. Dennis, P.G., Miller, A.J., Hirsch, P.R., 2010. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiology Ecology 72, 313-327. Eisenhauer, N., 2012. Aboveground-belowground interactions as a source of complementarity effects in biodiversity experiments. Plant and Soil 351, 1-22.

A new generic plant growth model framework (PMF): Simulating distributed dynamic interaction of biomass production and its interaction with water and nutrients fluxes

NASA Astrophysics Data System (ADS)

Multsch, Sebastian; Kraft, Philipp; Frede, Hans-Georg; Breuer, Lutz

2010-05-01

Today, crop models have a widespread application in natural sciences, because plant growth interacts and modifies the environment. Transport processes involve water and nutrient uptake from the saturated and unsaturated zone in the pedosphere. Turnover processes include the conversion of dead root biomass into organic matter. Transpiration and the interception of radiation influence the energy exchange between atmosphere and biosphere. But many more feedback mechanisms might be of interest, including erosion, soil compaction or trace gas exchanges. Most of the existing crop models have a closed structure and do not provide interfaces or code design elements for easy data transfer or process exchange with other models during runtime. Changes in the model structure, the inclusion of alternative process descriptions or the implementation of additional functionalities requires a lot of coding. The same is true if models are being upscaled from field to landscape or catchment scale. We therefore conclude that future integrated model developments would benefit from a model structure that has the following requirements: replaceability, expandability and independency. In addition to these requirements we also propose the interactivity of models, which means that models that are being coupled are highly interacting and depending on each other, i.e. the model should be open for influences from other independent models and react on influences directly. Hence, a model which consists of building blocks seems to be reasonable. The aim of the study is the presentation of the new crop model type, the plant growth model framework, PMF. The software concept refers to an object-oriented approach, which is developed with the Unified Modeling Language (UML). The model is implemented with Python, a high level object-oriented programming language. The integration of the models with a setup code enables the data transfer on the computer memory level and direct exchange of information about changing boundary conditions. The crop model concept refers to two main elements. A plant model, which represents an abstract network of plant organs and processes and a process library, which holds mathematical solutions for the growth processes. Growth processes were mainly taken from existing, well known crop models such as SUCROS and CERES. The crop specific properties of root architecture are described based on a maximum rooting depth and a vertical growth rate. The biomass distribution depends on an interactive allocation process due to the soil layers with a daily time step. In order to show the performance and capabilities of PMF, the model is coupled with the Catchment Modeling Framework (CMF) and the simple nitrogen mineralization model DeComp. The main feature of the integrated model set up is the interaction between root growth, water uptake and nitrogen supply of the soil. We show a virtual case study on the hillslope scale and spatially dependence of water and nitrogen stress based on topographic position and seasonal development.

Non-Invasive Methods to Characterize Soil-Plant Interactions at Different Scales

NASA Astrophysics Data System (ADS)

Javaux, M.; Kemna, A.; Muench, M.; Oberdoerster, C.; Pohlmeier, A.; Vanderborght, J.; Vereecken, H.

2006-05-01

Root water uptake is a dynamic and non-linear process, which interacts with the soil natural variability and boundary conditions to generate heterogeneous spatial distributions of soil water. Soil-root fluxes are spatially variable due to heterogeneous gradients and hydraulic connections between soil and roots. While 1-D effective representation of the root water uptake has been successfully applied to predict transpiration and average water content profiles, finer spatial characterization of the water distribution may be needed when dealing with solute transport. Indeed, root water uptake affects the water velocity field, which has an effect on solute velocity and dispersion. Although this variability originates from small-scale processes, these may still play an important role at larger scales. Therefore, in addition to investigate the variability of the soil hydraulic properties, experimental and numerical tools for characterizing root water uptake (and its effects on soil water distribution) from the pore to the field scales are needed to predict in a proper way the solute transport. Obviously, non-invasive and modeling techniques which are helpful to achieve this objective will evolve with the scale of interest. At the pore scale, soil structure and root-soil interface phenomena have to be investigated to understand the interactions between soil and roots. Magnetic resonance imaging may help to monitor water gradients and water content changes around roots while spectral induced polarization techniques may be used to characterize the structure of the pore space. At the column scale, complete root architecture of small plants and water content depletion around roots can be imaged by magnetic resonance. At that scale, models should explicitly take into account the three-dimensional gradient dependency of the root water uptake, to be able to predict solute transport. At larger scales however, simplified models, which implicitly take into account the heterogeneous root water uptake along roots, should be preferred given the complexity of the system. At such scales, electrical resistance tomography or ground-penetrating radar can be used to map the water content changes and derive effective parameters for predicting solute transport.

[Three dimensional fluorescent characteristics of soil dissolved organic matter (DOM) in Jiaozhou Bay coastal wetlands, China].

PubMed

Zi, Yuan Yuan; Kong, Fan Long; Xi, Min; Li, Yue; Yang, Ling

2016-12-01

In order to elucidate the structure characteristics of soil dissolved organic matter (DOM) and analyze the sources in Jiaozhou Bay coastal wetlands, four typical types of wetlands around Jiaozhou Bay were chosen, including Spartina anglica wetland, the barren wetland, Suaeda glauca wetland and Phragmites australis wetland. The soil samples were collected in January 2014. The contents of soil DOM were determined and the spectral analysis was made by three-dimensional fluorescent technology. The results showed that the contents of soil dissolved organic carbon (DOC) in four types of wetlands all decreased with the increasing soil depth, and S. anglica wetland ranked the first in the contents of soil DOC, followed by the barren wetland, S. glauca wetland and P. australis wetland. Five fluorescence peaks including B, T, A, D and C were found in the three-dimensional fluorescence spectrum (3DEEMs), indicating tyrosine-like, tryptophan-like, phenol-like, soluble microbial byproduct-like and humic acid-like- substances, respectively. Fluorescence integration (FRI) was applied in the qualitative analysis of five components. The results showed that tryptophan-like, phenol-like and tyrosine-like substances ranked in top three in content, followed by soluble microbial byproduct-like and humic acid-like substances which were not significantly different. Pearson correlation analysis demonstrated that a positive correlation existed between any two of the five components of DOM, and they were all positively related to DOC content. In addition, there existed different correlations between the five components of DOM and total phosphorus (TP), available phosphorus (AP) and total nitrogen (TN). The soil DOM in the four types of wetlands was mainly produced by biotic interactions, and the degree of humification was relatively low.

Soil Quality Indicator: a new concept

NASA Astrophysics Data System (ADS)

Barão, Lúcia; Basch, Gottlieb

2017-04-01

During the last century, cultivated soils have been intensively exploited for food and feed production. This exploitation has compromised the soils' natural functions and many of the soil-mediated ecosystems services, including its production potential for agriculture. Also, soils became increasingly vulnerable and less resilient to a wide range of threats. To overcome this situation, new and better management practices are needed to prevent soil from degradation. However, to adopt the best management practices in a specific location, it is necessary to evaluate the soil quality status first. Different soil quality indicators have been suggested over the last decades in order to evaluate the soil status, and those are often based on the performance of soil chemical, physical and biological properties. However, the direct link between these properties and the associated soil functions or soil vulnerability to threats appears more difficult to be established. This present work is part of the iSQAPER project- Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience, where new soil quality concepts are explored to provide better information regarding the effects of the most promising agricultural management practices on soil quality. We have developed a new conceptual soil quality indicator which determines the soil quality status, regarding its vulnerability towards different threats. First, different indicators were specifically developed for each of the eight threats considered - Erosion, SOM decline, Poor Structure, Poor water holding capacity, Compaction, N-Leaching, Soil-borne pests and diseases and Salinization. As an example for the case of Erosion, the RUSLE equation for the estimate of the soil annual loss was used. Secondly, a reference classification was established for each indicator to integrate all possible results into a Good, Intermediate or Bad classification. Finally, all indicators were combined to return a single evaluation of the soil status, using different techniques that are dependent on the final use of the soil quality indicator. Some of the advantages of this new concept include the evaluation of soil quality based on its vulnerability to threats, together with the evaluation of soil properties in a given context while also suggesting soil management practices that are directly capable to mitigate soil vulnerability towards specific threats. Keywords: Soil Quality, Agriculture, Sustainability, Soil threats

Ectomycorrhizal fungi and interspecific competition: species interactions, community structure, coexistence mechanisms, and future research directions.

PubMed

Kennedy, Peter

2010-09-01

The field of ectomycorrhizal fungal (EMF) ecology has largely developed outside the ecological mainstream, owing in large part to the challenges in studying the structure and dynamics of EMF communities. With advances in molecular identification and other research techniques, however, there has been growing interest among mycologists and ecologists in understanding how different ecological factors affect EMF community structure and diversity. While factors such as soil chemistry and host specificity have long been considered important, an increasing number of laboratory and field studies have documented that interspecific competition also has a major impact on EMF species interactions and may significantly influence EMF community structure. In this review, I examine the progress that has been made in understanding the nature of EMF competition. Currently, there are four conclusions that can be drawn: negative competitive effects are rarely reciprocal; competitive outcomes are environmentally context-dependent; field distributions often reflect competitive interactions; and timing of colonization influences competitive success. In addition, I highlight recent studies documenting links between competitive coexistence and EMF community structure, including checkerboard distributions, lottery models, storage effects, and colonization-competition tradeoffs. Finally, I discuss several aspects of EMF competition needing further investigation and some newer methods with which to address them.

Enhancing SMAP Soil Moisture Retrievals via Superresolution Techniques

NASA Astrophysics Data System (ADS)

Beale, K. D.; Ebtehaj, A. M.; Romberg, J. K.; Bras, R. L.

2017-12-01

Soil moisture is a key state variable that modulates land-atmosphere interactions and its high-resolution global scale estimates are essential for improved weather forecasting, drought prediction, crop management, and the safety of troop mobility. Currently, NASA's Soil Moisture Active/Passive (SMAP) satellite provides a global picture of soil moisture variability at a resolution of 36 km, which is prohibitive for some hydrologic applications. The goal of this research is to enhance the resolution of SMAP passive microwave retrievals by a factor of 2 to 4 using modern superresolution techniques that rely on the knowledge of high-resolution land surface models. In this work, we explore several super-resolution techniques including an empirical dictionary method, a learned dictionary method, and a three-layer convolutional neural network. Using a year of global high-resolution land surface model simulations as training set, we found that we are able to produce high-resolution soil moisture maps that outperform the original low-resolution observations both qualitatively and quantitatively. In particular, on a patch-by-patch basis we are able to produce estimates of high-resolution soil moisture maps that improve on the original low-resolution patches by on average 6% in terms of mean-squared error, and 14% in terms of the structural similarity index.

Soil microbial community profiles and functional diversity in limestone cedar glades

USGS Publications Warehouse

Cartwright, Jennifer M.; Dzantor, E. Kudjo; Momen, Bahram

2016-01-01

Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (< 25 cm), soil-moisture conditions fluctuate seasonally between xeric and saturated, and summer soil temperatures commonly exceed 48 °C. The effects of these stressors on soil microbial communities (SMC) remain largely unstudied, despite the importance of SMC-plant interactions in regulating the structure and function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles.

Impact of Soil Texture on Soil Ciliate Communities

NASA Astrophysics Data System (ADS)

Chau, J. F.; Brown, S.; Habtom, E.; Brinson, F.; Epps, M.; Scott, R.

2014-12-01

Soil water content and connectivity strongly influence microbial activities in soil, controlling access to nutrients and electron acceptors, and mediating interactions between microbes within and between trophic levels. These interactions occur at or below the pore scale, and are influenced by soil texture and structure, which determine the microscale architecture of soil pores. Soil protozoa are relatively understudied, especially given the strong control they exert on bacterial communities through predation. Here, ciliate communities in soils of contrasting textures were investigated. Two ciliate-specific primer sets targeting the 18S rRNA gene were used to amplify DNA extracted from eight soil samples collected from Sumter National Forest in western South Carolina. Primer sets 121F-384F-1147R (semi-nested) and 315F-959R were used to amplify soil ciliate DNA via polymerase chain reaction (PCR), and the resulting PCR products were analyzed by gel electrophoresis to obtain quantity and band size. Approximately two hundred ciliate 18S rRNA sequences were obtained were obtained from each of two contrasting soils. Sequences were aligned against the NCBI GenBank database for identification, and the taxonomic classification of best-matched sequences was determined. The ultimate goal of the work is to quantify changes in the ciliate community under short-timescale changes in hydrologic conditions for varying soil textures, elucidating dynamic responses to desiccation stress in major soil ciliate taxa.

A model of nitrous oxide evolution from soil driven by rainfall events. I - Model structure and sensitivity. II - Model applications

NASA Technical Reports Server (NTRS)

Changsheng, LI; Frolking, Steve; Frolking, Tod A.

1992-01-01

Simulations of N2O and CO2 emissions from soils were conducted with a rain-event driven, process-oriented model (DNDC) of nitrogen and carbon cycling processes in soils. The magnitude and trends of simulated N2O (or N2O + N2) and CO2 emissions were consistent with the results obtained in field experiments. The successful simulation of these emissions from the range of soil types examined demonstrates that the DNDC will be a useful tool for the study of linkages among climate, soil-atmosphere interactions, land use, and trace gas fluxes.

Using global sensitivity analysis to understand higher order interactions in complex models: an application of GSA on the Revised Universal Soil Loss Equation (RUSLE) to quantify model sensitivity and implications for ecosystem services management in Costa Rica

NASA Astrophysics Data System (ADS)

Fremier, A. K.; Estrada Carmona, N.; Harper, E.; DeClerck, F.

2011-12-01

Appropriate application of complex models to estimate system behavior requires understanding the influence of model structure and parameter estimates on model output. To date, most researchers perform local sensitivity analyses, rather than global, because of computational time and quantity of data produced. Local sensitivity analyses are limited in quantifying the higher order interactions among parameters, which could lead to incomplete analysis of model behavior. To address this concern, we performed a GSA on a commonly applied equation for soil loss - the Revised Universal Soil Loss Equation. USLE is an empirical model built on plot-scale data from the USA and the Revised version (RUSLE) includes improved equations for wider conditions, with 25 parameters grouped into six factors to estimate long-term plot and watershed scale soil loss. Despite RUSLE's widespread application, a complete sensitivity analysis has yet to be performed. In this research, we applied a GSA to plot and watershed scale data from the US and Costa Rica to parameterize the RUSLE in an effort to understand the relative importance of model factors and parameters across wide environmental space. We analyzed the GSA results using Random Forest, a statistical approach to evaluate parameter importance accounting for the higher order interactions, and used Classification and Regression Trees to show the dominant trends in complex interactions. In all GSA calculations the management of cover crops (C factor) ranks the highest among factors (compared to rain-runoff erosivity, topography, support practices, and soil erodibility). This is counter to previous sensitivity analyses where the topographic factor was determined to be the most important. The GSA finding is consistent across multiple model runs, including data from the US, Costa Rica, and a synthetic dataset of the widest theoretical space. The three most important parameters were: Mass density of live and dead roots found in the upper inch of soil (C factor), slope angle (L and S factor), and percentage of land area covered by surface cover (C factor). Our findings give further support to the importance of vegetation as a vital ecosystem service provider - soil loss reduction. Concurrent, progress is already been made in Costa Rica, where dam managers are moving forward on a Payment for Ecosystem Services scheme to help keep private lands forested and to improve crop management through targeted investments. Use of complex watershed models, such as RUSLE can help managers quantify the effect of specific land use changes. Moreover, effective land management of vegetation has other important benefits, such as bundled ecosystem services (e.g. pollination, habitat connectivity, etc) and improvements of communities' livelihoods.

Responses of redwood soil microbial community structure and N transformations to climate change

Treesearch

Damon C. Bradbury; Mary K. Firestone

2012-01-01

Soil microorganisms perform critical ecosystem functions, including decomposition, nitrogen (N) mineralization and nitrification. Soil temperature and water availability can be critical determinants of the rates of these processes as well as microbial community composition and structure. This research examined how changes in climate affect bacterial and fungal...

Change in physical structure of a phenol-spiked sapric histosol observed by Differential Scanning Calorimetry

NASA Astrophysics Data System (ADS)

Ondruch, Pavel; Kucerik, Jiri; Schaumann, Gabriele E.

2014-05-01

Interactions of pollutants with soil organic matter (SOM), their fate and transformation are crucial for understanding of soil functions and properties. In past, many papers dealing with sorption of organic and inorganic compounds have been published. However, their aim was almost exceptionally fo-cused on the pollutants themselves, determination of sorption isotherms and influence of external factors, while the change in SOM supramolecular structure was usually ignored. The SOM structure is, however, very important, since the adsorbed pollutant might have a significant influence on soil stability and functions. Differential scanning calorimetry (DSC) represents a technique, which has been successfully used to analyze the physical structure and physico-chemical aging of SOM. It has been found out that water molecules progressively stabilize SOM (water molecule bridge (WaMB)) (Schaumann & Bertmer 2008). Those bridges connect and stabilize SOM and can be disrupted at higher temperature (WaMB transition; (Kunhi Mouvenchery et al. 2013; Schaumann et al. 2013). In the same temperature region melting of aliphatic moieties can be observed (Hu et al. 2000; Chilom & Rice 2005; Kucerik et al. submitted 2013). In this work, we studied the effect of phenol on the physical structure of sapric histosol. Phenol was dissolved in various solvents (water, acetone, hexane, methanol) and added to soils. After the evaporation of solvents by air drying, the sample was equilibrated at 76% relative humidity for 3 weeks. Using DSC, we investigated the influence of phenol on histosol structure and time dependence of melting temperature of aliphatic moieties and WaMB transition. While addition of pure organic solvent only resulted in slightly increased transition temperatures, both melting temperature and WaMB transition temperature were significantly reduced in most cases if phenol was dissolved in these solvents. Water treatment caused a decrease in WaMB transition temperature but increased melting temperature. During the 150 days of physico-chemical aging, an increase in WaMB transition and melting temperature of aliphatic crystallites was was observed. Several types of treatments contrasting with this development were attributed to specific solvent -phenol interactions and will be discussed in this contribution. The results indicate that after introduction of phenol and during the consequent relaxation of the SOM structure, the re-formation of water molecule bridges is significantly reduced and decelerated. WaMB has been suggested as one SOM stabilizing mechanism (Schaumann & Bertmer 2008); the incorporation of phenol destabilizes the physical structure of SOM. It is assumed that phenol can penetrate into the WaMB hotspots, competes with water and/or disrupts WaMB or participate in WaMB formation. Simultaneously, phenol can penetrate and irreversibly change also the aliphatic crystallites, which are traditionally not considered being actively involved in sorption processes. It furthermore could compete with the organic matter for the hydration water. In this contribution, we will discuss these mechanisms. The results clearly demonstrate the potential of DSC to probe labile (physical) structures in soil organic matter and to elucidate interaction of organic chemicals with SOM moieties. References Chilom, G. & Rice, J.A. (2005). Glass transition and crystallite melting in natural organic matter. Organic Geochemistry, 36, 1339-1346. Hu, W.-G.; Mao, J.; Xing, B. & Schmidt-Rohr, K. (2000). Poly(methylene) crystallites in humic substances detected by Nuclear Magnetic Resonance. Environmental Science and Technology, 34, 530-534. Kucerik, J.; Schwarz, J.; Jaeger, A.; Bertmer, M. & Schaumann, G. (submitted 2013). Character of transitions causing physicochemical aging of a sapric histosol. Kunhi Mouvenchery, Y.; Jaeger, A.; Aquino, A.J.A.; Tunega, D.; Diehl, D.; Bertmer, M. & Schaumann, G.E. (2013). Restructuring of a peat in interaction with multivalent cations: Effect of cation type and aging time. PLoS ONE, 8, e65359. Schaumann, G.E. & Bertmer, M. (2008). Do water molecules bridge soil organic matter molecule segments? European Journal of Soil Science, 59, 423-429. Schaumann, G.E.; Gildemeister, D.; Kunhi Mouvenchery, Y.; Spielvogel, S. & Diehl, D. (2013). Interactions between cations and water molecule bridges in soil organic matter. Journal of Soils and Sediments, 13, 1579-1588.

The Role of Protein-Mineral Interactions for Protein Adsorption or Fragmentation

NASA Astrophysics Data System (ADS)

Chacon, S. S.; Reardon, P.; Washton, N.; Kleber, M.

2014-12-01

Soil exo-enzymes (EE) are proteins with the capability to catalyze the depolymerization of soil organic matter (SOM). SOM must be disassembled by EEs in order to be transported through the microbial cell wall and become metabolized. One factor determining an EE's functionality is their affinity to mineral surfaces found in the soil. Our goal was to establish the range of protein modifications, either chemical or structural, as the protein becomes associated with mineral surfaces. We hypothesized that pedogenic oxides would generate more extensive chemical alterations to the protein structure than phyllosilicates. A well-characterized protein proxy (Gb1, IEP 4.0, 6.2 kDA) was adsorbed onto functionally different mineral surfaces (goethite, montmorillonite, kaolinite and birnesite) at pH 5 and pH 7. We used 1H 15N Heteronuclear Single Quantum Coherence Nuclear Magnetic Resonance Spectroscopy (HSQC NMR) to observe structural modifications in the unadsorbed Gb1 that was allowed to equilibrate during the adsorption process for kaolinite, goethite and birnessite. Solid state NMR was used to observe the structural modifications of Gb1 while adsorbed onto kaolinite and montmorillonite. Preliminary results in the HSQC NMR spectra observed no changes in the native conformation of Gb1 when allowed to interact with goethite and kaolinite while birnessite induced strong structural modification of Gb1 at an acidic pH. Our results suggest that not all mineral surfaces in soil act as sorbents for EEs and changes in their catalytic activity upon adsorption to minerals surfaces may not just be an indication of conformational changes but of fragmentation of the protein itself.

Frequency- and Time-Domain Methods in Soil-Structure Interaction Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolisetti, Chandrakanth; Whittaker, Andrew S.; Coleman, Justin L.

2015-06-01

Soil-structure interaction (SSI) analysis in the nuclear industry is currently performed using linear codes that function in the frequency domain. There is a consensus that these frequency-domain codes give reasonably accurate results for low-intensity ground motions that result in almost linear response. For higher intensity ground motions, which may result in nonlinear response in the soil, structure or at the vicinity of the foundation, the adequacy of frequency-domain codes is unproven. Nonlinear analysis, which is only possible in the time domain, is theoretically more appropriate in such cases. These methods are available but are rarely used due to the largemore » computational requirements and a lack of experience with analysts and regulators. This paper presents an assessment of the linear frequency-domain code, SASSI, which is widely used in the nuclear industry, and the time-domain commercial finite-element code, LS-DYNA, for SSI analysis. The assessment involves benchmarking the SSI analysis procedure in LS-DYNA against SASSI for linearly elastic models. After affirming that SASSI and LS-DYNA result in almost identical responses for these models, they are used to perform nonlinear SSI analyses of two structures founded on soft soil. An examination of the results shows that, in spite of using identical material properties, the predictions of frequency- and time-domain codes are significantly different in the presence of nonlinear behavior such as gapping and sliding of the foundation.« less

Microbial mutualism at a distance: The role of geometry in diffusive exchanges

NASA Astrophysics Data System (ADS)

Peaudecerf, François J.; Bunbury, Freddy; Bhardwaj, Vaibhav; Bees, Martin A.; Smith, Alison G.; Goldstein, Raymond E.; Croze, Ottavio A.

2018-02-01

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.

The Role of Internal Standards and their Interaction with Soils Impact Accuracy of Volatile Organics Determinations

EPA Science Inventory

Both US Environmental Protection Agency (EPA) SW-846 Methods 8260C/5035 and 8261A include mixing soil with water and addition of internal standards prior to analyses but the equilibration of internal standards with the soil is not required. With increasing total organic carbon (...

Plant diversity and root traits benefit physical properties key to soil function in grasslands.

PubMed

Gould, Iain J; Quinton, John N; Weigelt, Alexandra; De Deyn, Gerlinde B; Bardgett, Richard D

2016-09-01

Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision. Here, in both a glasshouse and a long-term field study, we show that high plant diversity in grassland systems increases soil aggregate stability, a vital structural property of soil, and that root traits play a major role in determining diversity effects. We also reveal that the presence of particular plant species within mixed communities affects an even wider range of soil physical processes, including hydrology and soil strength regimes. Our results indicate that alongside well-documented effects on ecosystem functioning, plant diversity and root traits also benefit essential soil physical properties. © 2016 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Living part on soil bioengineering structures in Appennino Tosco-emiliano

NASA Astrophysics Data System (ADS)

Guastini, Enrico; Preti, Federico; Dani, Andrea

2014-05-01

From analisys headed up in soil bioengineered areas in different parts of Tuscany, the suitest root systems in slope stabilization turn out to be those spreading from seed-born plants, while adventitious roots from cuttings are often absent in the part more distant from the neck, and in some cases are insufficient to grant life support just in case of minor stress conditions. Genus Alnus shows it's adaptation capability to restore initial restoration steps and to create renovation prerequisites for other species through ammending litter production and symbiosis for nitrogen fixation with Frankia genus bacteria; other similar symbiosis (with Rhizobium and fungi) are carried out by Robinia pseudacacia. Soil fecundity increase is confirmed by the following entrance of more demanding species, as Ostrya carpinifolia and Acer pseudoplatanus at the tree level, Urtica dioica and Rubus Ulmifolius (nitrophilouses) at grass level. In the project phase it ought to imagine a well-structured implant, including rooted plants, cuttings and posibly a seed mix of colonising species aiming to form a germplasm on the structure itself in order to sprout whenever the local conditions allow it. Verifying that many after developed species came from ornithocore dissemination (Ficus carica, Pinus spp., Rosa canina, Sambucus nigra), lead to toughts about bedding out bird-attracting species on structures in order to realise a faster (and maybe more complex) succession development. This higher velocity could grant in a shorter period the production of a root mass spread in a more disomogeneous and complex pattern than that deriving from cuttings disposed in the traditional way; such a variability could allow a better interaction with other biological factors in the soil (bacteria, fungi, nematodes, ...) that are important for the plant nutrient cicle (Ohsowski et al., 2012) and then the constituion of an articulate, long-term system.

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages.

PubMed

Yang, Miao; Yang, Dan; Yu, Xuan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions.

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages

PubMed Central

Yang, Miao; Yang, Dan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions. PMID:29324845

The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

NASA Astrophysics Data System (ADS)

Rasche, Frank

2017-04-01

A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

Determination of soil degradation from flooding for estimating ecosystem services in Slovakia

NASA Astrophysics Data System (ADS)

Hlavcova, Kamila; Szolgay, Jan; Karabova, Beata; Kohnova, Silvia

2015-04-01

Floods as natural hazards are related to soil health, land-use and land management. They not only represent threats on their own, but can also be triggered, controlled and amplified by interactions with other soil threats and soil degradation processes. Among the many direct impacts of flooding on soil health, including soil texture, structure, changes in the soil's chemical properties, deterioration of soil aggregation and water holding capacity, etc., are soil erosion, mudflows, depositions of sediment and debris. Flooding is initiated by a combination of predispositive and triggering factors and apart from climate drivers it is related to the physiographic conditions of the land, state of the soil, land use and land management. Due to the diversity and complexity of their potential interactions, diverse methodologies and approaches are needed for describing a particular type of event in a specific environment, especially in ungauged sites. In engineering studies and also in many rainfall-runoff models, the SCS-CN method has remained widely applied for soil and land use-based estimations of direct runoff and flooding potential. The SCS-CN method is an empirical rainfall-runoff model developed by the USDA Natural Resources Conservation Service (formerly called the Soil Conservation Service or SCS). The runoff curve number (CN) is based on the hydrological soil characteristics, land use, land management and antecedent saturation conditions of soil. Since the method and curve numbers were derived on the basis of an empirical analysis of rainfall-runoff events from small catchments and hillslope plots monitored by the USDA, the use of the method for the conditions of Slovakia raises uncertainty and can cause inaccurate results in determining direct runoff. The objective of the study presented (also within the framework of the EU-FP7 RECARE Project) was to develop the SCS - CN methodology for the flood conditions in Slovakia (and especially for the RECARE pilot site of Myjava), with an emphasis on the determination of soil degradation from flooding for estimating ecosystem services. The parameters of the SCS-CN methodology were regionalised empirically based on actual rainfall and discharge measurements. Since there has been no appropriate methodology provided for the regionalisation of SCS-CN method parameters in Slovakia, such as runoff curve numbers and initial abstraction coefficients (λ), the work presented is important for the correct application of the SCS-CN method in our conditions.

Altering recharge dynamics through woody vegetation removal: a study on the Carrizo-Wilcox aquifer of south Texas

NASA Astrophysics Data System (ADS)

Mattox, A. M.

2011-12-01

Grasslands in many semi-arid regions of the world have seen an expansion of woody vegetation over the past century and many now exist largely as woodlands or shrublands. This "woody encroachment" results in numerous changes to ecosystem function, including alteration of element and water cycles. As in many parts of the world, these shrublands in south Texas have been subjected to a variety of management practices intended to reduce woody vegetation and increase the dominance of herbaceous vegetation. In addition to the intended change in vegetation structure, this activity has the potential to affect hydrologic fluxes and potentially increase deep drainage through reduced transpiration and rooting depths. However, there is significant uncertainty about the hydrologic response of vegetation to woody vegetation removal. We report here the results of a large manipulative experiment designed to assess the effects of woody vegetation removal on soil moisture movement in the vadose zone in an area that serves as a recharge zone for an unconsolidated sediment aquifer (Carrizo-Wilcox). In this study woody vegetation has been removed using a mechanical method (roller chopping) as well as a mechanical and chemical method (chainsaw removal + stump herbicide). The treated plots are located on three different soil types that represent the range of soils typical in this area. A water balance approach is used to assess soil moisture fluxes and potential deep drainage. In this first year of the study we quantified ecological and edaphic components that have the greatest effect on deep drainage, namely rooting depth, soil texture and antecedent soil water conditions. Exceptionally dry conditions this year have provided a unique opportunity to understand plant soil water interactions in the critical zone given the strong soil moisture limitations observed in the surface soil horizons. Understanding these interactions across different plant communities and soil textures are the initial steps to determining if ground water recharge may be increased through brush management. Rooting depth and volumetric water content were determined in the Chacon clay loam, Webb sandy loam and Antosa-Bobillo loamy sands. Two soil cores were taken to depths of 2 m in each of the 1/4 acre plots in each of the treated and untreated plots for a total of 54 cores. Rooting depths were determined through a combination of hydro-pneumatic root elutriation, comparison of soil water profiles in treated and untreated plots, as well as stem and soil water isotope analysis. Initial data indicates hydraulic redistribution is occurring in the loamy sand as well as the clay loam soils. Neutron probe measurements suggest that vegetation may be facilitating the movement of water into deeper soil horizons in the clay loam soils. In addition to improving our understanding of the relationships between vegetation structure and vadose zone hydrology, our results will be useful for managing water resources under increasing demand, climate change, and varied priorities for entities tasked with managing water resources.

Analysis of a Floodplain I-Wall Embedded in Horizontally Stratified Soil Layers During Flood Events Using Corps I-Wall Software Version 1.0

DTIC Science & Technology

2016-07-01

and gap propagation engineering methodology implemented within the software (CI-Wall) makes use of a hydraulic fracturing criterion, as discussed in...moist unit weight). Soil unit weights: Because of the presence of the upper moist (i.e, non - saturated) region R01 clay layer that is immediately...from two series of complete soil-structure interaction (SSI) non - linear finite element studies for I-Walls at New Orleans and other locations

FLUORESCENT IN SITU HYBRIDIZATION AND MICROAUTORADIOGRAPHY APPLIED TO ECOPHYSIOLOGY IN SOIL

EPA Science Inventory

Soil microbial communities perform many important processes, including nutrient cycling, plant-microorganism interactions, and degradation of xenobiotics. The study of microbial communities, however, has been limited by cultural methods, which may greatly underestimate diversity....

Soil Functional Zone Management: A Vehicle for Enhancing Production and Soil Ecosystem Services in Row-Crop Agroecosystems.

PubMed

Williams, Alwyn; Kane, Daniel A; Ewing, Patrick M; Atwood, Lesley W; Jilling, Andrea; Li, Meng; Lou, Yi; Davis, Adam S; Grandy, A Stuart; Huerd, Sheri C; Hunter, Mitchell C; Koide, Roger T; Mortensen, David A; Smith, Richard G; Snapp, Sieglinde S; Spokas, Kurt A; Yannarell, Anthony C; Jordan, Nicholas R

2016-01-01

There is increasing global demand for food, bioenergy feedstocks and a wide variety of bio-based products. In response, agriculture has advanced production, but is increasingly depleting soil regulating and supporting ecosystem services. New production systems have emerged, such as no-tillage, that can enhance soil services but may limit yields. Moving forward, agricultural systems must reduce trade-offs between production and soil services. Soil functional zone management (SFZM) is a novel strategy for developing sustainable production systems that attempts to integrate the benefits of conventional, intensive agriculture, and no-tillage. SFZM creates distinct functional zones within crop row and inter-row spaces. By incorporating decimeter-scale spatial and temporal heterogeneity, SFZM attempts to foster greater soil biodiversity and integrate complementary soil processes at the sub-field level. Such integration maximizes soil services by creating zones of 'active turnover', optimized for crop growth and yield (provisioning services); and adjacent zones of 'soil building', that promote soil structure development, carbon storage, and moisture regulation (regulating and supporting services). These zones allow SFZM to secure existing agricultural productivity while avoiding or minimizing trade-offs with soil ecosystem services. Moreover, the specific properties of SFZM may enable sustainable increases in provisioning services via temporal intensification (expanding the portion of the year during which harvestable crops are grown). We present a conceptual model of 'virtuous cycles', illustrating how increases in crop yields within SFZM systems could create self-reinforcing feedback processes with desirable effects, including mitigation of trade-offs between yield maximization and soil ecosystem services. Through the creation of functionally distinct but interacting zones, SFZM may provide a vehicle for optimizing the delivery of multiple goods and services in agricultural systems, allowing sustainable temporal intensification while protecting and enhancing soil functioning.

Soil Functional Zone Management: A Vehicle for Enhancing Production and Soil Ecosystem Services in Row-Crop Agroecosystems

PubMed Central

Williams, Alwyn; Kane, Daniel A.; Ewing, Patrick M.; Atwood, Lesley W.; Jilling, Andrea; Li, Meng; Lou, Yi; Davis, Adam S.; Grandy, A. Stuart; Huerd, Sheri C.; Hunter, Mitchell C.; Koide, Roger T.; Mortensen, David A.; Smith, Richard G.; Snapp, Sieglinde S.; Spokas, Kurt A.; Yannarell, Anthony C.; Jordan, Nicholas R.

2016-01-01

There is increasing global demand for food, bioenergy feedstocks and a wide variety of bio-based products. In response, agriculture has advanced production, but is increasingly depleting soil regulating and supporting ecosystem services. New production systems have emerged, such as no-tillage, that can enhance soil services but may limit yields. Moving forward, agricultural systems must reduce trade-offs between production and soil services. Soil functional zone management (SFZM) is a novel strategy for developing sustainable production systems that attempts to integrate the benefits of conventional, intensive agriculture, and no-tillage. SFZM creates distinct functional zones within crop row and inter-row spaces. By incorporating decimeter-scale spatial and temporal heterogeneity, SFZM attempts to foster greater soil biodiversity and integrate complementary soil processes at the sub-field level. Such integration maximizes soil services by creating zones of ‘active turnover’, optimized for crop growth and yield (provisioning services); and adjacent zones of ‘soil building’, that promote soil structure development, carbon storage, and moisture regulation (regulating and supporting services). These zones allow SFZM to secure existing agricultural productivity while avoiding or minimizing trade-offs with soil ecosystem services. Moreover, the specific properties of SFZM may enable sustainable increases in provisioning services via temporal intensification (expanding the portion of the year during which harvestable crops are grown). We present a conceptual model of ‘virtuous cycles’, illustrating how increases in crop yields within SFZM systems could create self-reinforcing feedback processes with desirable effects, including mitigation of trade-offs between yield maximization and soil ecosystem services. Through the creation of functionally distinct but interacting zones, SFZM may provide a vehicle for optimizing the delivery of multiple goods and services in agricultural systems, allowing sustainable temporal intensification while protecting and enhancing soil functioning. PMID:26904043

From peds to paradoxes: Linkages between soil biota and their influences on ecological processes

Treesearch

David C. Coleman

2008-01-01

Soils and their biota have been studied by a variety of observational and experimental methods that have allowed biologists to infer their structural and functional interactions. Viewing progress made over the last 10 years, it is apparent that an increasing diversity of analytical and chemical methods are providing much more detailed information about feeding...

Engineering Challenges for Closed Ecological System facilities

NASA Astrophysics Data System (ADS)

Dempster, William; Nelson, Mark; Allen, John P.

2012-07-01

Engineering challenges for closed ecological systems include methods of achieving closure for structures of different materials, and developing methods of allowing energy (for heating and cooling) and information transfer through the materially closed structure. Methods of calculating degree of closure include measuring degradation rates of inert trace gases introduced into the system. An allied problem is developing means of locating where leaks are located so that they may be repaired and degree of closure maintained. Once closure is achieved, methods of dealing with the pressure differentials between inside and outside are needed: from inflatable structures which might adjust to the pressure difference to variable volume chambers attached to the life systems component. These issues are illustrated through the engineering employed at Biosphere 2, the Biosphere 2 Test Module and the Laboratory Biosphere and a discussion of methods used by other closed ecological system facility engineers. Ecological challenges include being able to handle faster cycling rates and accentuated daily and seasonal fluxes of critical life elements such as carbon dioxide, oxygen, water, macro- and mico-nutrients. The problems of achieving sustainability in closed systems for life support include how to handle atmospheric dynamics including trace gases, producing a complete human diet and recycling nutrients and maintaining soil fertility, healthy air and water and preventing the loss of crucial elements from active circulation. In biospheric facilities the challenge is also to produce analogue to natural biomes and ecosystems, studying processes of self-organization and adaptation in systems that allow specification or determination of state variables and cycles which may be followed through all interactions from atmosphere to soils.

Lack of host specificity leads to independent assortment of dipterocarps and ectomycorrhizal fungi across a soil fertility gradient.

PubMed

Peay, Kabir G; Russo, Sabrina E; McGuire, Krista L; Lim, Zhenyu; Chan, Ju Ping; Tan, Sylvester; Davies, Stuart J

2015-08-01

Plants interact with a diversity of microorganisms, and there is often concordance in their community structures. Because most community-level studies are observational, it is unclear if such concordance arises because of host specificity, in which microorganisms or plants limit each other's occurrence. Using a reciprocal transplant experiment, we tested the hypothesis that host specificity between trees and ectomycorrhizal fungi determines patterns of tree and fungal soil specialisation. Seedlings of 13 dipterocarp species with contrasting soil specialisations were seeded into plots crossing soil type and canopy openness. Ectomycorrhizal colonists were identified by DNA sequencing. After 2.5 years, we found no evidence of host specificity. Rather, soil environment was the primary determinant of ectomycorrhizal diversity and composition on seedlings. Despite their close symbiosis, our results show that ectomycorrhizal fungi and tree communities in this Bornean rain forest assemble independently of host-specific interactions, raising questions about how mutualism shapes the realised niche. © 2015 John Wiley & Sons Ltd/CNRS.

Fall cover crops boost soil arbuscular mycorrhizal fungi which can lead to reduced inputs

USDA-ARS?s Scientific Manuscript database

Fall cover crops provide multiple benefits to producers. These benefits include pathogen and pest protection, drought protection, weed control, reduced soil erosion, nutrient acquisition and retention, increased soil organic matter, and conservation of soil water by improvement of soil structure th...

Fluorescence lifetime evaluation of whole soils from the Amazon rainforest.

PubMed

Nicolodelli, Gustavo; Tadini, Amanda Maria; Nogueira, Marcelo Saito; Pratavieira, Sebastião; Mounier, Stephane; Huaman, Jose Luis Clabel; Dos Santos, Cléber Hilário; Montes, Célia Regina; Milori, Débora Marcondes Bastos Pereira

2017-08-20

Time-resolved fluorescence spectroscopy (TRFS) is a new tool that can be used to investigate processes of interaction between metal ions and organic matter (OM) in soils, providing a specific analysis of the structure and dynamics of macromolecules. To the best of our knowledge, there are no studies in the literature reporting the use of this technique applied to whole/non-fractionated soil samples, making it a potential method for use in future studies. This work describes the use of TRFS to evaluate the fluorescence lifetimes of OM of whole soils from the Amazon region. Analysis was made of pellets of soils from an oxisol-spodosol system, collected in São Gabriel da Cachoeira (Amazonas, Brazil). The fluorescence lifetimes in the oxisol-spodosol system were attributed to two different fluorophores. One was related to complexation of an OM fraction with metals, resulting in a shorter fluorophore lifetime. A short fluorescence lifetime (2-12 ns) could be associated with simpler structures of the OM, while a long lifetime (19-66 ns) was associated with more complex OM structures. This new TRFS technique for analysis of the fluorescence lifetime in whole soil samples complies with the principles of green chemistry.

Subacute toxicity of copper and glyphosate and their interaction to earthworm (Eisenia fetida).

PubMed

Zhou, Chui-Fan; Wang, Yu-Jun; Li, Cheng-Cheng; Sun, Rui-Juan; Yu, Yuan-Chun; Zhou, Dong-Mei

2013-09-01

Glyphosate (GPS) and copper (Cu) are common pollutants in soils, and commonly co-exist. Due to the chemical structure of GPS, it can form complexes of heavy metals and interface their bioavailability in soil environment. In order to explore the interactions between GPS and Cu, subacute toxicity tests of Cu and GPS on soil invertebrate earthworms (Eisenia fetida) were conducted. The relative weight loss and whole-worm metal burdens increased significantly with the increasing exposure concentration of Cu, while the toxicity of GPS was insignificant. The joint toxicity data showed that the relative weight loss and the uptake of Cu, as well as the superoxide dismutase, catalase and malondialdehyde activities, were significantly alleviated in the present of GPS, which indicated that GPS could reduce the toxicity and bioavailability of Cu in the soil because of its strong chelating effects. Copyright © 2013 Elsevier Ltd. All rights reserved.

Soil Organic Matter (SOM): Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Amity

Molecular simulation is a powerful tool used to gain an atomistic, molecular, and nanoscale level understanding of the structure, dynamics, and interactions from adsorption on minerals and assembly in aggregates of soil organic matter (SOM). Given the importance of SOM fate and persistence in soils and the current knowledge gaps, applications of atomistic scale simulations to study the complex compounds in SOM and their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types common in soils are few and far between. Here, we describe various molecular simulation methods that are currently inmore » use in various areas and applicable to SOM research, followed by a brief survey of specific applications to SOM research and an illustration with our own recent efforts in this area. We conclude with an outlook and the challenges for future research in this area.« less

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

PubMed Central

Kim, Minsu; Or, Dani

2016-01-01

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

Application of Bioorganic Fertilizer Significantly Increased Apple Yields and Shaped Bacterial Community Structure in Orchard Soil.

PubMed

Wang, Lei; Li, Jing; Yang, Fang; E, Yaoyao; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2017-02-01

Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter and Rhodospirillaceae, were found to be the significantly increased by the BOF addition and the genus Lysobacter may identify members of this group effective in biological control-based plant disease management and the members of family Rhodospirillaceae had an important role in fixing molecular nitrogen. These results strengthen the understanding of responses to the BOF and possible interactions within bacterial communities in soil that can be associated with disease suppression and the accumulation of carbon and nitrogen. The increase of apple yields after the application of BOF might be attributed to the fact that the application of BOF increased SOM, and soil total nitrogen, and changed the bacterial community by enriching Rhodospirillaceae, Alphaprotreobateria, and Proteobacteria.

Plant Interactions with Changes in Coverage of Biological Soil Crusts and Water Regime in Mu Us Sandland, China

PubMed Central

Gao, Shuqin; Pan, Xu; Cui, Qingguo; Hu, Yukun; Ye, Xuehua; Dong, Ming

2014-01-01

Plant interactions greatly affect plant community structure. Dryland ecosystems are characterized by low amounts of unpredictable precipitation as well as by often having biological soil crusts (BSCs) on the soil surface. In dryland plant communities, plants interact mostly as they compete for water resources, and the direction and intensity of plant interaction varies as a function of the temporal fluctuation in water availability. Since BSCs influence water redistribution to some extent, a greenhouse experiment was conducted to test the hypothesis that the intensity and direction of plant interactions in a dryland plant community can be modified by BSCs. In the experiment, 14 combinations of four plant species (Artemisia ordosica, Artemisia sphaerocephala, Chloris virgata and Setaria viridis) were subjected to three levels of coverage of BSCs and three levels of water supply. The results show that: 1) BSCs affected plant interaction intensity for the four plant species: a 100% coverage of BSCs significantly reduced the intensity of competition between neighboring plants, while it was highest with a 50% coverage of BSCs in combination with the target species of A. sphaerocephala and C. virgata; 2) effects of the coverage of BSCs on plant interactions were modified by water regime when the target species were C. virgata and S. viridis; 3) plant interactions were species-specific. In conclusion, the percent coverage of BSCs affected plant interactions, and the effects were species-specific and could be modified by water regimes. Further studies should focus on effects of the coverage of BSCs on plant-soil hydrological processes. PMID:24498173

Plant interactions with changes in coverage of biological soil crusts and water regime in Mu Us Sandland, China.

PubMed

Gao, Shuqin; Pan, Xu; Cui, Qingguo; Hu, Yukun; Ye, Xuehua; Dong, Ming

2014-01-01

Plant interactions greatly affect plant community structure. Dryland ecosystems are characterized by low amounts of unpredictable precipitation as well as by often having biological soil crusts (BSCs) on the soil surface. In dryland plant communities, plants interact mostly as they compete for water resources, and the direction and intensity of plant interaction varies as a function of the temporal fluctuation in water availability. Since BSCs influence water redistribution to some extent, a greenhouse experiment was conducted to test the hypothesis that the intensity and direction of plant interactions in a dryland plant community can be modified by BSCs. In the experiment, 14 combinations of four plant species (Artemisia ordosica, Artemisia sphaerocephala, Chloris virgata and Setaria viridis) were subjected to three levels of coverage of BSCs and three levels of water supply. The results show that: 1) BSCs affected plant interaction intensity for the four plant species: a 100% coverage of BSCs significantly reduced the intensity of competition between neighboring plants, while it was highest with a 50% coverage of BSCs in combination with the target species of A. sphaerocephala and C. virgata; 2) effects of the coverage of BSCs on plant interactions were modified by water regime when the target species were C. virgata and S. viridis; 3) plant interactions were species-specific. In conclusion, the percent coverage of BSCs affected plant interactions, and the effects were species-specific and could be modified by water regimes. Further studies should focus on effects of the coverage of BSCs on plant-soil hydrological processes.

Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops

USDA-ARS?s Scientific Manuscript database

In this report we use Terminal Restriction Fragment Length Polymorphisms (TRFLP) in a tomato production system to “finger printing” the soil microbial community structure with Phylum specific primer sets. Factors influencing the soil microbes are a cover crop of Hairy Vetch (Vicia villosa) or Rye (...

Spatial and seasonal variations in mercury methylation and microbial community structure in a historic mercury mining area, Yolo County, California

USGS Publications Warehouse

Holloway, J.M.; Goldhaber, M.B.; Scow, K.M.; Drenovsky, R.E.

2009-01-01

The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Upland and wetland soils, stream sediments and tailings were collected and analyzed for nutrients (DOC, SO4=, NO3-), Hg, MeHg, and phospholipid fatty acids (PLFA). Stream sediment was derived from serpentinite, siltstone, volcanic rocks and mineralized serpentine with cinnabar, metacinnabar and other Hg phases. Soils from different parent materials had distinct PLFA biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of MeHg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. The greatest concentrations of MeHg (> 0.5??ng g- 1 MeHg) were measured in wetland soils and soil with a volcanic parent (9.5-37????g g- 1 Hg). Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation. Statistical models of the data demonstrated that soil microbial communities varied more with soil type than with season.

What can molecular dynamics simulations reveal about the stability of proteinaceous soil organic matter on mineral surfaces?

NASA Astrophysics Data System (ADS)

Andersen, A.; Reardon, P. N.; Chacon, S. S.; Qafoku, N. P.; Washton, N.; Kleber, M.

2015-12-01

With the increased attention on climate change and the role of increasing atmospheric CO2 levels in global warming, the need for an accurate depiction of the carbon cycling processes involved in the Earth's three major carbon pools, i.e., atmosphere, terrestrial systems, and oceans has never been greater. Within the terrestrial system, soil organic matter (SOM) represents an important carbon sub-pool. Complexation of SOM with mineral interfaces and particles is believed to protect SOM from possible biotic and abiotic transformation and mineralization to carbon dioxide. However, obtaining a molecular scale picture of the interactions of the various types of SOM with a variety of soil minerals is a challenging endeavor, especially for experimental techniques. Molecular scale simulations techniques can be applied to study the atomistic, molecular, and nanoscale aspects of SOM-mineral associations, and, therefore, and aid in filling current knowledge gaps in the potential fate and stability of SOM in soil systems. Here, we will discuss our recent results from large-scale molecular dynamics simulation of protein, GB1, and its interaction with clay and oxide/hydroxide minerals (i.e., kaolinite, Na+-MMT, Ca2+-MMT, goethite, and birnessite) including a comparison of structural changes of the protein by, protein orientation with respect to, degree of protein binding to, and mobility on the mineral surfaces. Our molecular simulations indicate that these mineral surfaces, with the exception of birnessite, potentially preserve the physical properties of the GB1 protein.

Natural succession on abandoned cropland effectively decreases the soil erodibility and improves the fungal diversity.

PubMed

Zhang, Chao; Liu, Guobin; Song, Zilin; Qu, Dong; Fang, Linchuan; Deng, Lei

2017-10-01

Changes in plants and soils during natural succession have been evaluated, but little is known about the effects of succession on the activities of soil microbes and their interactions with soil erodibility. We conducted a field study on the Chinese Loess Plateau, typical of this semiarid area, to determine the effect of secondary succession on the stability of soil structure against erosion and on the composition of soil fungal communities. Characteristics of plant, soil, and fungal communities were assessed across a 30-yr chronosequence of grassland developed from abandoned cropland. The diversity and composition of the fungal communities were determined using high-throughput sequencing of the internal transcribed spacer. Six grasslands were selected to represent different successional age classes: 0 (cropland), 5, 10, 15, 20, and 30 yr. Short-term decreases (initial 5 yr) in the amounts of soil organic carbon, total nitrogen, available phosphorus, and fungal biomass and in fungal diversity had returned to original levels (i.e., cropland) within 15 yr and were much higher after continued succession. Abandoning cropland for succession caused the soil erodibility (K) decrease and the aboveground coverage, soil nutrient levels, content of larger (>5 mm) water-stable aggregate, mean aggregate weight diameter, and diversity of the fungal communities improvement including arbuscular mycorrhizas (AMF), ectomycorrhizas (EMF), and saprotrophs. The fungal communities were dominated by Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota during the succession. The successional patterns of the plant and fungal communities were similar, although distinct fungal communities were not observed in the two initial stages, suggesting that fungal succession may develop more slowly than plant succession. Plant root biomass, EMF, and soil organic carbon content accounted for most of the variation of soil erodibility (28.6%, 19.5%, and 11.8%, respectively), indicating their importance in shaping soil structure to prevent erosion. Our results demonstrated that abandoning cropland for natural succession could decrease soil erodibility and increase fungal diversity. EMF plays an important role in soil stability against erosion in the Loess Plateau. Abandoning cropland for natural succession should be recommended for alleviating soil erosion and improving the degraded soils in this area. © 2017 by the Ecological Society of America.

Earthworm impacts on organo-mineral interactions and soil carbon inventories in Fennoscandian boreal and sub-arctic landscapes

NASA Astrophysics Data System (ADS)

Wackett, Adrian; Yoo, Kyungsoo; Cameron, Erin; Klaminder, Jonatan

2017-04-01

Boreal and sub-arctic environments sustain some of the most pristine and fragile ecosystems in the world and house a disproportionate amount of the global soil carbon pool. Although the historical view of soil carbon turnover has focused on the intrinsic molecular structure of organic matter, recent work has highlighted the importance of stabilizing soil carbon on reactive mineral surfaces. However, the rates and mechanisms controlling these processes at high latitudes are poorly understood. Here we explored the biogeochemical impacts of deep-burrowing earthworm species on a range of Fennoscandian forest soils to investigate how earthworms impact soil carbon inventories and organo-mineral associations across boreal and sub-arctic landscapes. We sampled soils and earthworms at six sites spanning almost ten degrees latitude and encompassing a wide range of soil types and textures, permitting simultaneous consideration of how climate and mineralogy affect earthworm-mediated shifts in soil carbon dynamics. Across all sites, earthworms significantly decreased the carbon and nitrogen contents of the upper 10 cm, presumably through consumption of the humus layer and subsequent incorporation of the underlying mineral soil into upper organic horizons. Their mixing of humus and underlying soil also generally increased the proportion of mineral surface area occluded by organic matter, although the extent to which earthworms facilitate such organo-mineral interactions appears to be controlled by soil texture and mineralogy. This work indicates that quantitative measurements of mineral surface area and its extent of coverage by soil organic matter facilitate scaling up of molecular interactions between organic matter and minerals to the level of soil profiles and landscapes. Our preliminary data also strongly suggests that earthworms have profound effects on the fate of soil carbon and nitrogen in boreal and sub-arctic environments, highlighting the need for a better understanding of the joint ecological impacts of warming and indirect disturbances like earthworm introduction by humans to make sound predictions of future ecosystem change and carbon-climate feedbacks.

Molecular aspects of aromatic C additions to soils: Implications of char quality for ecosystem functionality

NASA Astrophysics Data System (ADS)

Keiluweit, M.; Nico, P. S.; Johnson, M. G.; Kleber, M.

2009-12-01

Solid residues of incomplete combustion (biochar or char) are continuously being added to soils due to natural vegetation fires in many ecosystems. However, new strategies for carbon sequestration in soils are likely to include the active addition of biochar to soils. Since biochar is a highly aromatic organic material such additions will modify the native molecular structure of soil organic matter and thus alter interactions with the global atmosphere and hydrosphere. Here we present a molecular level assessment of the physical organization and chemical complexity of biomass-derived chars and, specifically, that of aromatic carbon in char structures. Differences among wood and grass charred at temperatures from 100 to 700°C are investigated. BET-N2 surface area, X-ray diffraction (XRD), synchrotron-based Near-edge X-ray Absorption Fine Structure (NEXAFS) and Fourier transform infrared (FT-IR) spectroscopy results demonstrate how the two plant precursor materials undergo analogous, but quantitatively different physical-chemical transitions as charring intensity increases. These changes suggest the existence of four distinct physical and chemical categories of char. We find that each category of char consists of a unique mixture of chemical phases and physical states: (i) in transition chars the crystalline character of the precursor materials is preserved, (ii) in amorphous chars the heat-altered molecules and incipient aromatic polycondensates are randomly mixed, (iii) composite chars consist of poorly ordered graphene stacks embedded in amorphous phases, and (iv) turbostratic chars are dominated by turbostratic (disordered) graphitic crystallites. There is wide variation in both the chemical and the physical nature of aromatic carbon among these char categories. In this presentation we will point out how molecular variations among the aromatic components of the different char categories translate into differences in their ability to: (i) persist in the environment, (ii) function as environmental sorbents, and (iii) to enable the soil to provide environmental services.

Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp.

NASA Astrophysics Data System (ADS)

Otten, Wilfred; Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Spiers, Andrew; Baveye, Philippe

2017-04-01

The way micro-organisms access C and interact with each other in heterogeneous environments is key to our understanding of soil processes. Growth and mobility of bacteria is crucial aspect of these processes in particular how this is affected by complicated pathways of water and air-filled pores. Simplified experimental systems, often referred to with the term microcosms, have played a central role in the development of modern ecological thinking ranging from competitive exclusion to examination of spatial resources and competitive mechanisms, with important model driven insights to the field. However, in the majority of cases these do not include detailed description of the soil physical conditions and hence there is still little insight in how soil structure affects these processes. Recent advances in the use of Xray CT now allow for a different approach to this as we can obtain quantitative insight in to the pathways of interaction and how these are controlled in microcosms. In the current presentation we therefor ask the following questions: - To what extent can we control the pore geometry in microcosm studies through manipulation of common variables such as density and aggregate size? Are replicated microcosms really replicated at the microscale? - What is the effect of pore geometry on the growth dynamics of bacteria following introduction into soil? - What is the effect of pore geometry on the rate and extent of spread of bacteria in soil? We focus on Pseudomonas sp. and Bacillus sp. Both species are abundantly present in the rhizosphere and bulk-soil, frequently studied for their growth promoting ability, yet there is still very little knowledge available on how the growth and spread is affected by soil physical conditions such as pore geometry and wetness. We show how pore geometry, connectivity and interface areas are affected by the way soil is packed into microcosms and how this affects growth and spread of both species. We emphasize that microscopic heterogeneity has significant impact on bacterial dynamics and that soil physical conditions need to be considered in greater detail in microcosm studies to ensure generalisation of results.

Energy Dissipation in Earthquake Soil Structure Interaction: The September 3rd, 2016 M5.8 Pawnee Oklahoma Earthquake

NASA Astrophysics Data System (ADS)

Yang, H.; Sinha, S. K.; Feng, Y.; Jeremic, B.

2016-12-01

The M5.8 earthquake occurred in Pawnee, Oklahoma on September 3rd 2016 is the strongest seismic event recorded in Oklahoma. Soil structure interaction (SSI) played an important role in this tragic event. As a major aspect of SSI analysis, the propagation and dissipation of seismic energy will be studied in depth, with particular focus on the ground motion recorded in this earthquake. Seismic energy propagates from seismic source to the SSI system and is dissipated within and around the SSI system. Energy dissipation with the SSI system is related to inelastic behavior of soil, rock, contact zone (foundation-soil/rock), structural components and energy dissipators. Accurate evaluation of seismic energy can be used to optimize SSI system for safety and economy. The SSI system can be designed so that majority of seismic energy is dissipated within soil and soil-foundation contact zone, away from the structure.Accurate and theoretically sound modeling of propagation and dissipation is essential to use of seismic energy for design and assessment. The rate of plastic work is defined as the product of stress and the rate of plastic strain. On the other hand, plastic dissipation is defined as a form of heat transfer. The difference between these two quantities, which has been neglected in many studies, is a plastic part of the free energy. By considering energy storage and dissipation at both micro (particle) scale and macro (continuum) scale, it can be shown that the plastic free energy is an intrinsic attribute at the continuum scale due to particle rearrangement. Proper application of thermodynamics to finite element simulations, plastic dissipation can be correctly modeled. Examples will be used to illustrate above point on both constitutive, single element and SSI model scales. In addition, propagation of seismic energy, its dissipation (timing and location) will be used to illustrate use in design and assessment.

Application of atomic force microscopy to the study of natural and model soil particles.

PubMed

Cheng, S; Bryant, R; Doerr, S H; Rhodri Williams, P; Wright, C J

2008-09-01

The structure and surface chemistry of soil particles has extensive impact on many bulk scale properties and processes of soil systems and consequently the environments that they support. There are a number of physiochemical mechanisms that operate at the nanoscale which affect the soil's capability to maintain native vegetation and crops; this includes soil hydrophobicity and the soil's capacity to hold water and nutrients. The present study used atomic force microscopy in a novel approach to provide unique insight into the nanoscale properties of natural soil particles that control the physiochemical interaction of material within the soil column. There have been few atomic force microscopy studies of soil, perhaps a reflection of the heterogeneous nature of the system. The present study adopted an imaging and force measurement research strategy that accounted for the heterogeneity and used model systems to aid interpretation. The surface roughness of natural soil particles increased with depth in the soil column a consequence of the attachment of organic material within the crevices of the soil particles. The roughness root mean square calculated from ten 25 microm(2) images for five different soil particles from a Netherlands soil was 53.0 nm, 68.0 nm, 92.2 nm and 106.4 nm for the respective soil depths of 0-10 cm, 10-20 cm, 20-30 cm and 30-40 cm. A novel analysis method of atomic force microscopy phase images based on phase angle distribution across a surface was used to interpret the nanoscale distribution of organic material attached to natural and model soil particles. Phase angle distributions obtained from phase images of model surfaces were found to be bimodal, indicating multiple layers of material, which changed with the concentration of adsorbed humic acid. Phase angle distributions obtained from phase images of natural soil particles indicated a trend of decreasing surface coverage with increasing depth in the soil column. This was consistent with previous macroscopic determination of the proportions of organic material chemically extracted from bulk samples of the soils from which specimen particles were drawn. Interaction forces were measured between atomic force microscopy cantilever tips (Si(3)N(4)) and natural soil and model surfaces. Adhesion forces at humic acid free specimen surfaces (Av. 20.0 nN), which are primarily hydrophilic and whose interactions are subject to a significant contribution from the capillary forces, were found to be larger than those of specimen surfaces with adsorbed humic acid (Av. 6.5 nN). This suggests that adsorbed humic acid increased surface hydrophobicity. The magnitude and distribution of adhesion forces between atomic force microscopy tips and the natural particle surfaces was affected by both local surface roughness and the presence of adsorbed organic material. The present study has correlated nanoscale measurements with established macroscale methods of soil study. Thus, the research demonstrates that atomic force microscopy is an important addition to soil science that permits a multiscale analysis of the multifactorial phenomena of soil hydrophobicity and wetting.

The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions

PubMed Central

Jacoby, Richard; Peukert, Manuela; Succurro, Antonella; Koprivova, Anna; Kopriva, Stanislav

2017-01-01

In their natural environment, plants are part of a rich ecosystem including numerous and diverse microorganisms in the soil. It has been long recognized that some of these microbes, such as mycorrhizal fungi or nitrogen fixing symbiotic bacteria, play important roles in plant performance by improving mineral nutrition. However, the full range of microbes associated with plants and their potential to replace synthetic agricultural inputs has only recently started to be uncovered. In the last few years, a great progress has been made in the knowledge on composition of rhizospheric microbiomes and their dynamics. There is clear evidence that plants shape microbiome structures, most probably by root exudates, and also that bacteria have developed various adaptations to thrive in the rhizospheric niche. The mechanisms of these interactions and the processes driving the alterations in microbiomes are, however, largely unknown. In this review, we focus on the interaction of plants and root associated bacteria enhancing plant mineral nutrition, summarizing the current knowledge in several research fields that can converge to improve our understanding of the molecular mechanisms underpinning this phenomenon. PMID:28974956

Soil ionomic and enzymatic responses and correlations to fertilizations amended with and without organic fertilizer in long-term experiments.

PubMed

Feng, Xumeng; Ling, Ning; Chen, Huan; Zhu, Chen; Duan, Yinghua; Peng, Chang; Yu, Guanghui; Ran, Wei; Shen, Qirong; Guo, Shiwei

2016-04-15

To investigate potential interactions between the soil ionome and enzyme activities affected by fertilization with or without organic fertilizer, soil samples were collected from four long-term experiments over China. Irrespective of variable interactions, fertilization type was the major factor impacting soil ionomic behavior and accounted for 15.14% of the overall impact. Sampling site was the major factor affecting soil enzymatic profile and accounted for 34.25% of the overall impact. The availabilities of Pb, La, Ni, Co, Fe and Al were significantly higher in soil with only chemical fertilizer than the soil with organic amendment. Most of the soil enzyme activities, including α-glucosidase activity, were significantly activated by organic amendment. Network analysis between the soil ionome and the soil enzyme activities was more complex in the organic-amended soils than in the chemical fertilized soils, whereas the network analysis among the soil ions was less complex with organic amendment. Moreover, α-glucosidase was revealed to generally harbor more corrections with the soil ionic availabilities in network. We concluded that some of the soil enzymes activated by organic input can make the soil more vigorous and stable and that the α-glucosidase revealed by this analysis might help stabilize the soil ion availability.

Soil ionomic and enzymatic responses and correlations to fertilizations amended with and without organic fertilizer in long-term experiments

PubMed Central

Feng, Xumeng; Ling, Ning; Chen, Huan; Zhu, Chen; Duan, Yinghua; Peng, Chang; Yu, Guanghui; Ran, Wei; Shen, Qirong; Guo, Shiwei

2016-01-01

To investigate potential interactions between the soil ionome and enzyme activities affected by fertilization with or without organic fertilizer, soil samples were collected from four long-term experiments over China. Irrespective of variable interactions, fertilization type was the major factor impacting soil ionomic behavior and accounted for 15.14% of the overall impact. Sampling site was the major factor affecting soil enzymatic profile and accounted for 34.25% of the overall impact. The availabilities of Pb, La, Ni, Co, Fe and Al were significantly higher in soil with only chemical fertilizer than the soil with organic amendment. Most of the soil enzyme activities, including α-glucosidase activity, were significantly activated by organic amendment. Network analysis between the soil ionome and the soil enzyme activities was more complex in the organic-amended soils than in the chemical fertilized soils, whereas the network analysis among the soil ions was less complex with organic amendment. Moreover, α-glucosidase was revealed to generally harbor more corrections with the soil ionic availabilities in network. We concluded that some of the soil enzymes activated by organic input can make the soil more vigorous and stable and that the α-glucosidase revealed by this analysis might help stabilize the soil ion availability. PMID:27079657

Priorities for research in soil ecology

PubMed Central

Eisenhauer, Nico; Antunes, Pedro M.; Bennett, Alison E.; Birkhofer, Klaus; Bissett, Andrew; Bowker, Matthew A.; Caruso, Tancredi; Chen, Baodong; Coleman, David C.; de Boer, Wietse; de Ruiter, Peter; DeLuca, Thomas H.; Frati, Francesco; Griffiths, Bryan S.; Hart, Miranda M.; Hättenschwiler, Stephan; Haimi, Jari; Heethoff, Michael; Kaneko, Nobuhiro; Kelly, Laura C.; Leinaas, Hans Petter; Lindo, Zoë; Macdonald, Catriona; Rillig, Matthias C.; Ruess, Liliane; Scheu, Stefan; Schmidt, Olaf; Seastedt, Timothy R.; van Straalen, Nico M.; Tiunov, Alexei V.; Zimmer, Martin; Powell, Jeff R.

2017-01-01

The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise. PMID:29129942

Priorities for research in soil ecology.

PubMed

Eisenhauer, Nico; Antunes, Pedro M; Bennett, Alison E; Birkhofer, Klaus; Bissett, Andrew; Bowker, Matthew A; Caruso, Tancredi; Chen, Baodong; Coleman, David C; de Boer, Wietse; de Ruiter, Peter; DeLuca, Thomas H; Frati, Francesco; Griffiths, Bryan S; Hart, Miranda M; Hättenschwiler, Stephan; Haimi, Jari; Heethoff, Michael; Kaneko, Nobuhiro; Kelly, Laura C; Leinaas, Hans Petter; Lindo, Zoë; Macdonald, Catriona; Rillig, Matthias C; Ruess, Liliane; Scheu, Stefan; Schmidt, Olaf; Seastedt, Timothy R; van Straalen, Nico M; Tiunov, Alexei V; Zimmer, Martin; Powell, Jeff R

2017-07-01

The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.

Soil Structure - A Neglected Component of Land-Surface Models

NASA Astrophysics Data System (ADS)

Fatichi, S.; Or, D.; Walko, R. L.; Vereecken, H.; Kollet, S. J.; Young, M.; Ghezzehei, T. A.; Hengl, T.; Agam, N.; Avissar, R.

2017-12-01

Soil structure is largely absent in most standard sampling and measurements and in the subsequent parameterization of soil hydraulic properties deduced from soil maps and used in Earth System Models. The apparent omission propagates into the pedotransfer functions that deduce parameters of soil hydraulic properties primarily from soil textural information. Such simple parameterization is an essential ingredient in the practical application of any land surface model. Despite the critical role of soil structure (biopores formed by decaying roots, aggregates, etc.) in defining soil hydraulic functions, only a few studies have attempted to incorporate soil structure into models. They mostly looked at the effects on preferential flow and solute transport pathways at the soil profile scale; yet, the role of soil structure in mediating large-scale fluxes remains understudied. Here, we focus on rectifying this gap and demonstrating potential impacts on surface and subsurface fluxes and system wide eco-hydrologic responses. The study proposes a systematic way for correcting the soil water retention and hydraulic conductivity functions—accounting for soil-structure—with major implications for near saturated hydraulic conductivity. Modification to the basic soil hydraulic parameterization is assumed as a function of biological activity summarized by Gross Primary Production. A land-surface model with dynamic vegetation is used to carry out numerical simulations with and without the role of soil-structure for 20 locations characterized by different climates and biomes across the globe. Including soil structure affects considerably the partition between infiltration and runoff and consequently leakage at the base of the soil profile (recharge). In several locations characterized by wet climates, a few hundreds of mm per year of surface runoff become deep-recharge accounting for soil-structure. Changes in energy fluxes, total evapotranspiration and vegetation productivity are less significant but they can reach up to 10% in specific locations. Significance for land-surface and hydrological modeling and implications for distributed domains are discussed.

Role of model structure on the response of soil biogeochemistry to hydro-climatic fluctuations

NASA Astrophysics Data System (ADS)

Manzoni, S.; Porporato, A.

2005-05-01

Soil carbon and nutrient cycles are strongly affected by hydro-climatic variability, which interacts with the internal ecosystem structure. Here we test the implications of biogeochemical model structure on such dynamics by extending an existing model by the authors and coworkers. When forced by hydro-climatic fluctuations, the different model structures induce specific preferential nutrient paths among the soil pools, which in turn affect nutrient distribution and availability to microbes and plants. In particular, if it is assumed that microbes can directly assimilate organic nitrogen, plants tend to be inferior competitors for nutrients even in well-watered conditions, while if a certain amount of organic nitrogen is assumed to be mineralized without being first incorporated into microbial cells, vegetation can be advantaged over a wide range of soil moisture values. We also investigate the intensification of competition for nutrients (e.g., nitrogen) between plant and soil microbial communities under extreme hydrologic conditions, such as droughts and intense storms. Frequent rainfall events may determine ideal soil moisture conditions for plant uptake, enhancing nitrogen leaching while lowering oxygen concentration and inhibiting microbial activity. During droughts, the soil water potential often drops to the point of hampering the plant nutrient uptake while still remaining high enough for microbial decomposition and nitrogen immobilization. The interplay of microbe and vegetation water stress is investigated in depth as it controls the ability of one community (e.g., plants or soil microbes) to establish competitive advantage on the other. The long-term effects of these dynamics of competition and nutrient allocation are explored under steady-state and stochastic soil moisture conditions to analyze the feedbacks between soil organic matter and vegetation dynamics.

(A)biotic processes control soil carbon dynamics: quantitative assessment of model complexity, stability and response to perturbations for improving ESMs

NASA Astrophysics Data System (ADS)

Georgiou, K.; Abramoff, R. Z.; Harte, J.; Riley, W. J.; Torn, M. S.

2016-12-01

As global temperatures and atmospheric CO2 concentrations continue to increase, soil microbial activity and decomposition of soil organic matter (SOM) are expected to follow suit, potentially limiting soil carbon storage. Traditional global- and ecosystem-scale models simulate SOM decomposition using linear kinetics, which are inherently unable to reproduce carbon-concentration feedbacks, such as priming of native SOM at elevated CO2 concentrations. Recent studies using nonlinear microbial models of SOM decomposition seek to capture these interactions, and several groups are currently integrating these microbial models into Earth System Models (ESMs). However, despite their widespread ability to exhibit nonlinear responses, these models vary tremendously in complexity and, consequently, dynamics. In this study, we explore, both analytically and numerically, the emergent oscillatory behavior and insensitivity of SOM stocks to carbon inputs that have been deemed `unrealistic' in recent microbial models. We discuss the sources of instability in four models of varying complexity, by sequentially reducing complexity of a detailed model that includes microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We also present an alternative representation of microbial turnover that limits population sizes and, thus, reduces oscillations. We compare these models to several long-term carbon input manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that traditional linear and nonlinear models cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures, and that modifying microbial turnover results in more realistic predictions. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in ESMs.

[Effect of agricultural application of municipal sewage sludge on plant-soil system: A review].

PubMed

Liu, Meng Jiao; Xia, Shao Pan; Wang, Jun; Ma, Qing Xu; Wang, Zhong Qiang; Wu, Liang Huan

2017-12-01

Currently, reasonable disposal of municipal sewage sludge is one of the important issues in the field of resources and environmental science. Sludge is rich in large amounts of organic matter and available nutrients, promoting soil fertility, soil physical structure and biological properties. However, sludge contains a variety of heavy metals, organic contaminants and other hazardous substance, especially heavy metals, which are the bottlenecks of agricultural application of sludge. To improve the sewage sludge utilization efficiency and decrease the effect on soil, this essay made a summary on domestic and foreign studies on plant-soil interaction ecosystem with sewage sludge to provide a theoretical basis and scientific guidance for advancing sewage sludge utilization efficiency.

Plant diversity effects on soil food webs are stronger than those of elevated CO2 and N deposition in a long-term grassland experiment

PubMed Central

Eisenhauer, Nico; Dobies, Tomasz; Cesarz, Simone; Hobbie, Sarah E.; Meyer, Ross J.; Worm, Kally; Reich, Peter B.

2013-01-01

Recent metaanalyses suggest biodiversity loss affects the functioning of ecosystems to a similar extent as other global environmental change agents. However, the abundance and functioning of soil organisms have been hypothesized to be much less responsive to such changes, particularly in plant diversity, than aboveground variables, although tests of this hypothesis are extremely rare. We examined the responses of soil food webs (soil microorganisms, nematodes, microarthropods) to 13-y manipulation of multiple environmental factors that are changing at global scales—specifically plant species richness, atmospheric CO2, and N deposition—in a grassland experiment in Minnesota. Plant diversity was a strong driver of the structure and functioning of soil food webs through several bottom-up (resource control) effects, whereas CO2 and N only had modest effects. We found few interactions between plant diversity and CO2 and N, likely because of weak interactive effects of those factors on resource availability (e.g., root biomass). Plant diversity effects likely were large because high plant diversity promoted the accumulation of soil organic matter in the site’s sandy, organic matter–poor soils. Plant diversity effects were not explained by the presence of certain plant functional groups. Our results underline the prime importance of plant diversity loss cascading to soil food webs (density and diversity of soil organisms) and functions. Because the present results suggest prevailing plant diversity effects and few interactions with other global change drivers, protecting plant diversity may be of high priority to maintain the biodiversity and functioning of soils in a changing world. PMID:23576722

Sorptive and desorptive fractionation of dissolved organic matter by mineral soil matrices.

PubMed

Oren, Adi; Chefetz, Benny

2012-01-01

Interactions of dissolved organic matter (DOM) with soil minerals, such as metal oxides and clays, involve various sorption mechanisms and may lead to sorptive fractionation of certain organic moieties. While sorption of DOM to soil minerals typically involves a degree of irreversibility, it is unclear which structural components of DOM correspond to the irreversibly bound fraction and which factors may be considered determinants. To assist in elucidating that, the current study aimed at investigating fractionation of DOM during sorption and desorption processes in soil. Batch DOM sorption and desorption experiments were conducted with organic matter poor, alkaline soils. Fourier-transform infrared (FTIR) and UV-Vis spectroscopy were used to analyze bulk DOM, sorbed DOM, and desorbed DOM fractions. Sorptive fractionation resulted mainly from the preferential uptake of aromatic, carboxylic, and phenolic moieties of DOM. Soil metal-oxide content positively affected DOM sorption and binding of some specific carboxylate and phenolate functional groups. Desorptive fractionation of DOM was expressed by the irreversible-binding nature of some carboxylic moieties, whereas other bound carboxylic moieties were readily desorbed. Inner-sphere, as opposed to outer-sphere, ligand-exchange complexation mechanisms may be responsible for these irreversible, as opposed to reversible, interactions, respectively. The interaction of aliphatic DOM constituents with soil, presumably through weak van der Waals forces, was minor and increased with increasing proportion of clay minerals in the soil. Revealing the nature of DOM-fractionation processes is of great importance to understanding carbon stabilization mechanisms in soils, as well as the overall fate of contaminants that might be associated with DOM. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Two factors defining humus as a key structural component of soil organic matter and as a physicochemical speciation of carbon in its turnover wending its way through the micro environment of soil, sediments and natural waters

NASA Astrophysics Data System (ADS)

Aleksandrova, Olga

2016-04-01

Over the last 40-50 years, the scientific community started to question the model of soil organic matter. Close consideration has been given to the following models: the classic model that regards a significant part of soil organic matter as large, covalently bonded 'humus polymers', which are formed via "humification", and the continuum model that considers soil organic matter as 'supra molecular aggregates of degradation fragments'[1]. The underlying cause of a contradiction between 'humus polymers' model and continuum model of SOM implies that 'the vast majority of operationally defined humic material in soils is a very complex mixture of microbial and plant biopolymers and their degradation products but not a distinct chemical category'. Furthermore, authors [1] of the continuum model suggested 'to turn to modern, evidence based concept, and to abandon the operational proxies of the past' that means to consider term 'humus' as an out-of-date model. However, micro cosmos of organic matter in soil implies not only an assemblage of molecular units but also a system of interactions of different types [2]. Peculiar interactions in SOM allow us to understand a lot of physicochemical phenomena observed in soil samples, for example by EPR and SL EPR examinations [3, 4, 5]. Among specific interactions in soil, mention should be made of hydrogen (H) bonds and hydrophobic interaction. Spin Labeling EPR examination of natural and labeled soil samples showed that in SOM, there are stable and roaming H-bonds. Stable H-bonds are typical of a part of SOM, which can be isolated as humus, whereas a non-humified part of SOM is rich in roaming hydrogen bonds. Addition of some water (more than maximal moisture) to soil leads to disintegration of some weak H-bond. Other solvents influence SOM the same way but they disintegrate stronger or weaker H-bonds in dependence on used solvent. Thus in soil, different environmental conditions (like moisture, temperature or pollution) influence on a change in the partitioning of roaming H-bonds, and in turn, define components, into which non-humified SOM can be disintegrated. Therefore, some physicochemical species of SOM, which can be observed in physicochemical processes of carbon turnover in soil, originate from disintegrated SOM bulged at the seams of weak H-bonds, and doesn't reveal strong properties of humus because humus structure is still bound to SOM via stronger H-bonds. Also, SL EPR examination of native and labeled soil samples revealed the substantial influence of hydrophobic interaction on physicochemical speciation of carbon in soil, and this interaction is mediated by humus [3]. Among different effects of hydrophobic interaction, the formation of condensed matter is of great interest. Condensed matter mediated by humic acids is shown to reveal specific quantum properties and invoke hydrodynamic instability on the surface of plant roots that results in uptake of the whole nano-pieces of humus by plant roots, as it was observed in [6, 7]. Considered effects of H-bonds with different bonding energy and hydrophobic interaction in SOM show that a carbon turnover in soil is mediated by humus, and humus play a substantial role as the physicochemical speciation in carbon turnover. Thus, model of 'humus' is still an up-to-date model. 1.Lehmann J. &Kleber H. (2015). Nature, 528, Issue 7580, 60 - 68. 2. M. Hutta, R. Gora, R. Halko, et al., (2011). J. Chromatogr. A., 1218, 8946. 3. Alexanderova O.N. (2015). J Soils Sediments, DOI 10.1007/s11368-015-1195-2 4. Aleksandrova O.N., Kholodov V.A., Perminova I.V. (2015). Russian Journal of Physical Chemistry A, 2015, Vol. 89, No. 8, pp. 1407-1413. 5. Aleksandrova O.N. (2013). J Geochem Explor 129:6-13. 6. Smirnov A.I. et al. (1991). J. of Magnetic Resonance 91, 386-391 7. Kulikova N.V. et al. (2012). Conference HIT-2012.

Soil-modified carbon paste electrode: a useful tool in environmental assessment of heavy metal ion binding interactions.

PubMed

Svegl, I G; Ogorevc, B

2000-08-01

Carbon paste electrodes (CPEs) modified with different soils in their native form were prepared to create a soil-like solid phase suitable for application in studies of heavy metal ion uptake and binding interactions. The preparation of CPEs modified with five different soils was examined and their heavy metal ion uptake behavior investigated using a model Cu(II) aqueous solution. Metal ions were accumulated under open circuit conditions and were determined after a medium exchange using differential pulse anodic stripping voltammetry, applying preelectrolysis at -0.7 V. The soil-modified CPE accumulation behavior, including the linearity of the current response versus Cu(II) concentration, the influence of the pH on the solution, and the uptake kinetics, was thoroughly investigated. The correlation between the soil-modified CPE uptake capability and the standard soil parameters, such as ion exchange capacity, soil pH, organic matter and clay content, were evaluated for all five examined soils. The influence of selected endogenous cations (K(I), Ca(II), Fe(III)) on the transfer of Cu(II) ions from a solution to the simulated soil solid phase was examined and is discussed. Preliminary examinations of the soil-modified CPE uptake behavior with some exogenous heavy metal ions of strong environmental interest (Pb(II), Hg(II), Cd(II) and Ag(I)) are also presented. This work demonstrates some attractive possibilities for the application of a soil-modified CPE in studying soil-heavy metal ion binding interactions, with a further potential use as a new environmental sensor appropriate for fist on-site testing of polluted soils.

Soil-plant interaction monitoring: Small scale example of an apple orchard in Trentino, North-Eastern Italy.

PubMed

Cassiani, Giorgio; Boaga, Jacopo; Rossi, Matteo; Putti, Mario; Fadda, Giuseppe; Majone, Bruno; Bellin, Alberto

2016-02-01

Accurate monitoring and modeling of soil-plant systems are a key unresolved issue that currently limits the development of a comprehensive view of the interactions between soil and atmosphere, with a number of practical consequences including the difficulties in predicting climatic change patterns. This paper presents a case study where time-lapse minimal-invasive 3D micro-electrical tomography (ERT) is used to monitor rhizosphere eco-hydrological processes in an apple orchard in the Trentino region, Northern Italy. In particular we aimed at gaining a better understanding of the soil-vegetation water exchanges in the shallow critical zone, as part of a coordinated effort towards predicting climate-induced changes on the hydrology of Mediterranean basins (EU FP7 CLIMB project). The adopted strategy relied upon the installation of a 3D electrical tomography apparatus consisting of four mini-boreholes carrying 12 electrodes each plus 24 mini-electrodes on the ground surface, arranged in order to image roughly a cubic meter of soil surrounding a single apple tree. The monitoring program was initially tested with repeated measurements over about one year. Subsequently, we performed three controlled irrigation tests under different conditions, in order to evaluate the water redistribution under variable root activities and climatic conditions. Laboratory calibration on soil samples allowed us to translate electrical resistivity variations into moisture content changes, supported also by in-situ TDR measurements. Richards equation modeling was used also to explain the monitoring evidence. The results clearly identified the effect of root water uptake and the corresponding subsoil region where active roots are present, but also marked the need to consider the effects of different water salinity in the water infiltration process. We also gained significant insight about the need to measure quantitatively the plant evapotranspiration in order to close the water balance and separate soil structure effects (primarily, hydraulic conductivity) from water dynamics induced by living plants. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of earthworms and plants on the soil structure, the physical stabilization of soil organic matter and the microbial abundance and diversity in soil aggregates in a long term study

NASA Astrophysics Data System (ADS)

Zangerlé, Anne; Hissler, Christophe; Lavelle, Patrick

2014-05-01

Earthworms and plant roots, as ecosystem engineers, have large effects on biotic and abiotic properties of the soil system. They create biogenic soil macroaggregates (i.e. earthworm casts and root macroaggregates) with specific physical, chemical and microbiological properties. Research to date has mainly considered their impacts in isolation thereby ignoring potential interactions between these organisms. On the other hand, most of the existing studies focused on short to midterm time scale. We propose in this study to consider effect of earthworms and plants on aggregate dynamics at long time scale. A 24 months macrocosm experiment, under semi-controlled conditions, was conducted to assess the impacts of corn and endogeic plus anecic earthworms (Apporectodea caliginosa and Lumbricus terrestris) on soil structure, C stabilization and microbial abundance and biodiversity. Aggregate stability was assessed by wet-sieving. Macroaggregates (>2 mm) were also visually separated according to their biological origin (e.g., earthworms, roots). Total C and N contents were measured in aggregates of all size classes and origins. Natural abundances of 13C of corn, a C4 plant, were used as a supplemental marker of OM incorporation in aggregates. The genetic structure and the abundance of the bacterial and fungal communities were characterized by using respectively the B- and F-ARISA fingerprinting approach and quantitative PCR bacteria (341F/515R) and fungi (FF330/FR1). They significantly impacted the soil physical properties in comparison to the other treatments: lower bulk density in the first 10cm of the soil with 0.95 g/cm3 in absence of corn plants and 0.88 g/cm3 in presence of corn plants compared to control soil (1.21g/cm3). The presence of earthworms increased aggregate stability (mean weight diameter) by 7.6 %, while plants alone had no simple impacts on aggregation. A significant interaction revealed that earthworms increased aggregate stability in the presence of roots by 2.4% when compared to macrocosms without plants. Additionally, the presence of roots increased the total C and N concentration in earthworm casts, while earthworms increased C storage in microaggregates within root-derived aggregates. Analyses of 13C abundances revealed that OM had been incorporated in earthworm casts from the fifth month of the experiment. Earthworms showed an impact on bacterial abundance of 26.7% of increase in single species macroaggregates and 35.5% in mixt species macroaggregates after the first harvest of corn plants. Trends however changed on the long term since bacterial abundances decreased dramatically (67.1% in single species treatments and 59.3% in mixed species treatments) during the second year and fungal abundances, stable during the first 5 months of the experiment, later increased 80% and 73.2% in earthworm and mixed species macroaggregates. This experiment showed how interactions between plants and earthworms can influence the soil structure and the soil aggregates dynamics by cooperating in macroaggregate formation. Both organisms need to be considered simultaneously for proper management of soils.

Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

USGS Publications Warehouse

Cartwright, Jennifer M.; Advised by Dzantor, E. Kudjo

2015-01-01

Stress factors quantified by this research include shallow soil (depth to bedrock ranging from 2.4 to 22.6 cm), volumetric soil water content levels seasonally ranging from xeric (below 5%) to saturated (above 50%), and seasonally extreme ground-surface temperatures (above 48°C). Findings from this research indicate that spatial and temporal heterogeneity exists in limestone cedar glades in terms of abiotic stress factors and soil physical and chemical properties. Several such soil properties (e.g. soil depth, organic matter levels, pH, and particle size distribution) are spatially correlated. These soil properties were statistically related to ecological structures and functions such as vegetation patterns, soil respiration, the density of culturable heterotrophic microbes in soil and metabolic diversity of soil microbial community profiles. In general, zones within limestone cedar glades that had relatively shallow soil, alkaline pH, low levels of organic matter and high levels of silt also tended to have depressed rates of soil respiration and reduced densities and metabolic diversity of culturable heterotrophic soil microbes. Additionally, seasonally-relevant stress factors including soil water content and temperatures at or near the soil surface were related to the same set of ecological structures and functions.

Method and apparatus for optimized sampling of volatilizable target substances

DOEpatents

Lindgren, Eric R.; Phelan, James M.

2004-10-12

An apparatus for capturing, from gases such as soil gas, target analytes. Target analytes may include emanations from explosive materials or from residues of explosive materials. The apparatus employs principles of sorption common to solid phase microextraction, and is best used in conjunction with analysis means such as a gas chromatograph. To sorb target analytes, the apparatus functions using various sorptive structures to capture target analyte. Depending upon the embodiment, those structures may include a capillary tube including an interior surface on which sorptive material (similar to that on the surface of a SPME fiber) is supported (along with means for moving gases through the capillary tube so that the gases come into close proximity to the sorptive material). In one disclosed embodiment, at least one such sorptive structure is associated with an enclosure including an opening in communication with the surface of a soil region potentially contaminated with buried explosive material such as unexploded ordnance. Emanations from explosive materials can pass into and accumulate in the enclosure where they are sorbed by the sorptive structures. Also disclosed is the use of heating means such as microwave horns to drive target analytes into the soil gas from solid and liquid phase components of the soil.

What's so critical about the critical zone?: New insights at the boundaries between hydrology, pedology, geomorphology, rocks and life (Invited)

NASA Astrophysics Data System (ADS)

Grant, G.

2013-12-01

The great promise of critical zone science and observatories (CZOs) emerging over the past decade was that real progress towards understanding the earth's near-surface environment could be made through coordinated studies of processes and interactions that occur within that thin layer between the bottom of the atmosphere and the top of competent bedrock - the critical zone. How well has this promise been realized, and where is the science now headed? Drawing on recent findings from CZOs and elsewhere, I identify a number of exciting and potentially transformative new ideas and threads at the boundaries of hydrology, geomorphology, pedology, and ecology. These include: 1). New understanding of interactions and feedbacks among soil weathering, pathways for water, tree roots, and bedrock fractures. A fundamental insight emerging from critical zone studies is that soils are far more interestingly structured than simple textbook models of homogeneous substrates with exponentially decreasing permeability with depth. Instead, the near-surface is now seen as a complex network of voids, paths, conduits, and storage zones that are both formed and exploited by the movement of water, geochemical reactions, and organisms. This evolving perspective on the critical zone has implications for a wide range of issues, including the residence time and chemistry of water, rates of weathering, slope stability, and long-term soil fertility. 2. Growing appreciation for the role of biology in conditioning and transforming its own physical environment within the critical zone. This includes the role of trees in hydraulically redistributing water, fracturing bedrock, and contributing to long-term soil erosion and landscape evolution through tree fall and throw and vegetation effects on moisture regimes. 3. Similarly, the importance of understanding linkages among soils, water, and vegetation has never been greater as a warming climate dramatically changes the 'rules of the game'. New understanding of feedbacks among vegetation growth and water uptake, soil moisture regimes, snowpack dynamics, and overall forest health are challenging previous assumptions about how best to manage forest environments in the face of a warming atmosphere and increased frequencies of disturbance. Time will tell whether these new perspectives represent incremental or fundamental shifts in our thinking about the critical zone, but it is clearly an exciting time for critical zone science and scientists.

Plant traits related to nitrogen uptake influence plant-microbe competition.

PubMed

Moreau, Delphine; Pivato, Barbara; Bru, David; Busset, Hugues; Deau, Florence; Faivre, Céline; Matejicek, Annick; Strbik, Florence; Philippot, Laurent; Mougel, Christophe

2015-08-01

Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more relevant for understanding plant-microbe interactions than composite traits, such as nitrophily, which are related to a number of ecophysiological processes.

The role of plant-microbiome interactions in weed establishment and control.

PubMed

Trognitz, Friederike; Hackl, Evelyn; Widhalm, Siegrid; Sessitsch, Angela

2016-10-01

The soil microbiome plays an important role in the establishment of weeds and invasive plants. They associate with microorganisms supporting their growth and health. Weed management strategies, like tillage and herbicide treatments, to control weeds generally alter soil structure going alongside with changes in the microbial community. Once a weed population establishes in the field, the plants build up a close relationship with the available microorganisms. Seeds or vegetative organs overwinter in soil and select early in the season their own microbiome before crop plants start to vegetate. Weed and crop plants compete for light, nutrition and water, but may differently interact with soil microorganisms. The development of new sequencing technologies for analyzing soil microbiomes has opened up the possibility for in depth analysis of the interaction between 'undesired' plants and crop plants under different management systems. These findings will help us to understand the functions of microorganisms involved in crop productivity and plant health, weed establishment and weed prevention. Exploitation of the knowledge offers the possibility to search for new biocontrol methods against weeds based on soil and plant-associated microorganisms. This review discusses the recent advances in understanding the functions of microbial communities for weed/invasive plant establishment and shows new ways to use plant-associated microorganisms to control weeds and invasive plants in different land management systems. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Achieving Closure for Bioregenerative Life Support Systems: Engineering and Ecological Challenges, Research Opportunities

NASA Astrophysics Data System (ADS)

Dempster, William; Allen, John P.

Closed systems are desirable for a number of purposes: space life support systems where precious life-supporting resources need to be kept inside; biospheric systems; where global ecological pro-cesses can be studied in great detail and testbeds where research topics requiring isolation from the outside (e.g. genetically modified organisms; radioisotopes) can be studied in isolation from the outside environment and where their ecological interactions and fluxes can be studied. But to achieve and maintain closure raises both engineering and ecological challenges. Engineering challenges include methods of achieving closure for structures of different materials, and devel-oping methods of allowing energy (for heating and cooling) and information transfer through the materially closed structure. Methods of calculating degree of closure include measuring degradation rates of inert trace gases introduced into the system. An allied problem is devel-oping means of locating where leaks are located so that they may be repaired and degree of closure maintained. Once closure is achieved, methods of dealing with the pressure differen-tials between inside and outside are needed: from inflatable structures which might adjust to the pressure difference to variable volume chambers attached to the life systems component. These issues are illustrated through the engineering employed at Biosphere 2, the Biosphere 2 Test Module and the Laboratory Biosphere and a discussion of methods used by other closed ecological system facility engineers. Ecological challenges include being able to handle faster cycling rates and accentuated daily and seasonal fluxes of critical life elements such as carbon dioxide, oxygen, water, macro-and mico-nutrients. The problems of achieving sustainability in closed systems for life support include how to handle atmospheric dynamics including trace gases, producing a complete human diet and recycling nutrients and maintaining soil fertility, healthy air and water and preventing the loss of crucial elements from active circulation. In biospheric facilities the challenge is also to produce analogue to natural biomes and ecosys-tems, studying processes of self-organization and adaptation in systems that allow specification or determination of state variables and cycles which may be followed through all interactions from atmosphere to soils.

The AgroEcoSystem (AgES) response-function model simulates layered soil water dynamics in semi-arid Colorado: sensitivity and calibration

USDA-ARS?s Scientific Manuscript database

Simulation of vertical soil hydrology is a critical component of simulating even more complex soil water dynamics in space and time, including land-atmosphere and subsurface interactions. The AgroEcoSystem (AgES) model is defined here as a single land unit implementation of the full AgES-W (Watershe...

Site productivity and diversity of the Middle Mountain long-term soil productivity study, West Virginia: Pre-experimental site characterization

Treesearch

Mary Beth Adams

2018-01-01

To better understand the impacts of a changing environment and interactions with forest management options for forest resources, including soil, large long-term experiments are required. Such experiments require careful documentation of reference or pre-experimental conditions. This publication describes the Middle Mountain Long-term Soil Productivity (LTSP) Study,...

Permafrost and organic layer interactions over a climate gradient in a discontinuous permafrost zone

NASA Astrophysics Data System (ADS)

Johnson, Kristofer D.; Harden, Jennifer W.; McGuire, A. David; Clark, Mark; Yuan, Fengming; Finley, Andrew O.

2013-09-01

Permafrost is tightly coupled to the organic soil layer, an interaction that mediates permafrost degradation in response to regional warming. We analyzed changes in permafrost occurrence and organic layer thickness (OLT) using more than 3000 soil pedons across a mean annual temperature (MAT) gradient. Cause and effect relationships between permafrost probability (PF), OLT, and other topographic factors were investigated using structural equation modeling in a multi-group analysis. Groups were defined by slope, soil texture type, and shallow (<28 cm) versus deep organic (≥28 cm) layers. The probability of observing permafrost sharply increased by 0.32 for every 10-cm OLT increase in shallow OLT soils (OLTs) due to an insulation effect, but PF decreased in deep OLT soils (OLTd) by 0.06 for every 10-cm increase. Across the MAT gradient, PF in sandy soils varied little, but PF in loamy and silty soils decreased substantially from cooler to warmer temperatures. The change in OLT was more heterogeneous across soil texture types—in some there was no change while in others OLTs soils thinned and/or OLTd soils thickened at warmer locations. Furthermore, when soil organic carbon was estimated using a relationship with thickness, the average increase in carbon in OLTd soils was almost four times greater compared to the average decrease in carbon in OLTs soils across all soil types. If soils follow a trajectory of warming that mimics the spatial gradients found today, then heterogeneities of permafrost degradation and organic layer thinning and thickening should be considered in the regional carbon balance.

Permafrost and organic layer interactions over a climate gradient in a discontinuous permafrost zone

USGS Publications Warehouse

Johnson, Kristofer D.; Harden, Jennifer W.; McGuire, A. David; Clark, Mark; Yuan, Fengming; Finley, Andrew O.

2013-01-01

Permafrost is tightly coupled to the organic soil layer, an interaction that mediates permafrost degradation in response to regional warming. We analyzed changes in permafrost occurrence and organic layer thickness (OLT) using more than 3000 soil pedons across a mean annual temperature (MAT) gradient. Cause and effect relationships between permafrost probability (PF), OLT, and other topographic factors were investigated using structural equation modeling in a multi-group analysis. Groups were defined by slope, soil texture type, and shallow (<28 cm) versus deep organic (≥28 cm) layers. The probability of observing permafrost sharply increased by 0.32 for every 10-cm OLT increase in shallow OLT soils (OLTs) due to an insulation effect, but PF decreased in deep OLT soils (OLTd) by 0.06 for every 10-cm increase. Across the MAT gradient, PF in sandy soils varied little, but PF in loamy and silty soils decreased substantially from cooler to warmer temperatures. The change in OLT was more heterogeneous across soil texture types—in some there was no change while in others OLTs soils thinned and/or OLTd soils thickened at warmer locations. Furthermore, when soil organic carbon was estimated using a relationship with thickness, the average increase in carbon in OLTd soils was almost four times greater compared to the average decrease in carbon in OLTs soils across all soil types. If soils follow a trajectory of warming that mimics the spatial gradients found today, then heterogeneities of permafrost degradation and organic layer thinning and thickening should be considered in the regional carbon balance.

Selenium deficiency risk predicted to increase under future climate change

PubMed Central

Jones, Gerrad D.; Droz, Boris; Greve, Peter; Gottschalk, Pia; Poffet, Deyan; McGrath, Steve P.; Seneviratne, Sonia I.; Smith, Pete; Winkel, Lenny H. E.

2017-01-01

Deficiencies of micronutrients, including essential trace elements, affect up to 3 billion people worldwide. The dietary availability of trace elements is determined largely by their soil concentrations. Until now, the mechanisms governing soil concentrations have been evaluated in small-scale studies, which identify soil physicochemical properties as governing variables. However, global concentrations of trace elements and the factors controlling their distributions are virtually unknown. We used 33,241 soil data points to model recent (1980–1999) global distributions of Selenium (Se), an essential trace element that is required for humans. Worldwide, up to one in seven people have been estimated to have low dietary Se intake. Contrary to small-scale studies, soil Se concentrations were dominated by climate–soil interactions. Using moderate climate-change scenarios for 2080–2099, we predicted that changes in climate and soil organic carbon content will lead to overall decreased soil Se concentrations, particularly in agricultural areas; these decreases could increase the prevalence of Se deficiency. The importance of climate–soil interactions to Se distributions suggests that other trace elements with similar retention mechanisms will be similarly affected by climate change. PMID:28223487

Selenium deficiency risk predicted to increase under future climate change.

PubMed

Jones, Gerrad D; Droz, Boris; Greve, Peter; Gottschalk, Pia; Poffet, Deyan; McGrath, Steve P; Seneviratne, Sonia I; Smith, Pete; Winkel, Lenny H E

2017-03-14

Deficiencies of micronutrients, including essential trace elements, affect up to 3 billion people worldwide. The dietary availability of trace elements is determined largely by their soil concentrations. Until now, the mechanisms governing soil concentrations have been evaluated in small-scale studies, which identify soil physicochemical properties as governing variables. However, global concentrations of trace elements and the factors controlling their distributions are virtually unknown. We used 33,241 soil data points to model recent (1980-1999) global distributions of Selenium (Se), an essential trace element that is required for humans. Worldwide, up to one in seven people have been estimated to have low dietary Se intake. Contrary to small-scale studies, soil Se concentrations were dominated by climate-soil interactions. Using moderate climate-change scenarios for 2080-2099, we predicted that changes in climate and soil organic carbon content will lead to overall decreased soil Se concentrations, particularly in agricultural areas; these decreases could increase the prevalence of Se deficiency. The importance of climate-soil interactions to Se distributions suggests that other trace elements with similar retention mechanisms will be similarly affected by climate change.

Soil Oxidation-Reduction in Wetlands and Its Impact on Plant Functioning

PubMed Central

Pezeshki, S. R.; DeLaune, R. D.

2012-01-01

Soil flooding in wetlands is accompanied by changes in soil physical and chemical characteristics. These changes include the lowering of soil redox potential (Eh) leading to increasing demand for oxygen within the soil profile as well as production of soil phytotoxins that are by-products of soil reduction and thus, imposing potentially severe stress on plant roots. Various methods are utilized for quantifying plant responses to reducing soil conditions that include measurement of radial oxygen transport, plant enzymatic responses, and assessment of anatomical/morphological changes. However, the chemical properties and reducing nature of soil environment in which plant roots are grown, including oxygen demand, and other associated processes that occur in wetland soils, pose a challenge to evaluation and comparison of plant responses that are reported in the literature. This review emphasizes soil-plant interactions in wetlands, drawing attention to the importance of quantifying the intensity and capacity of soil reduction for proper evaluation of wetland plant responses, particularly at the process and whole-plant levels. Furthermore, while root oxygen-deficiency may partially account for plant stress responses, the importance of soil phytotoxins, produced as by-products of low soil Eh conditions, is discussed and the need for development of methods to allow differentiation of plant responses to reduced or anaerobic soil conditions vs. soil phytotoxins is emphasized. PMID:24832223

Representing biophysical landscape interactions in soil models by bridging disciplines and scales.

NASA Astrophysics Data System (ADS)

van der Ploeg, M. J.; Carranza, C.; Teixeira da Silva, R.; te Brake, B.; Baartman, J.; Robinson, D.

2017-12-01

The combination of climate change, population growth and soil threats including carbon loss, biodiversity decline and erosion, increasingly confront the global community (Schwilch et al., 2016). One major challenge in studying processes involved in soil threats, landscape resilience, ecosystem stability, sustainable land management and resulting economic consequences, is that it is an interdisciplinary field (Pelletier et al., 2012). Less stringent scientific disciplinary boundaries are therefore important (Liu et al., 2007), because as a result of disciplinary focus, ambiguity may arise on the understanding of landscape interactions. This is especially true in the interaction between a landscape's physical and biological processes (van der Ploeg et al. 2012). Biophysical landscape interactions are those biotic and abiotic processes in a landscape that have an influence on the developments within and evolution of a landscape. An important aspect in biophysical landscape interactions is the differences in scale related to the various processes that play a role in these systems. Moreover, the interplay between the physical landscape and the occurring vegetation, which often co-evolve, and the resulting heterogeneity and emerging patterns are the reason why it is so challenging to establish a theoretical basis to describe biophysical processes in landscapes (e.g. te Brake et al. 2013, Robinson et al. 2016). Another complicating factor is the response of vegetation to changing environmental conditions, including a possible, and often unknown, time-lag (e.g. Metzger et al., 2009). An integrative description for modelling biophysical interactions has been a long standing goal in soil science (Vereecken et al., 2016). We need the development of soil models that are more focused on networks, connectivity and feedbacks incorporating the most important aspects of our detailed mechanistic modelling (Paola & Leeder, 2011). Additionally, remote sensing measurement techniques facilitate non-interfering observation of biophysical interactions on a landscape scale. A joint effort to connect Earth's (sub)surface processes by a combination of innovative big data-assimilation, measurement and modelling techniques will enable the scientific community to accurately address vital issues.

Biologically-Mediated Weathering of Minerals From Nanometre Scale to Environmental Systems

NASA Astrophysics Data System (ADS)

Brown, D. J.; Banwart, S. A.; Smits, M. M.; Leake, J. R.; Bonneville, S.; Benning, L. G.; Haward, S. J.; Ragnarsdottir, K.

2007-12-01

The Weathering Science Consortium is a multi-disciplinary project that aims to create a step change in understanding how biota control mineral weathering and soil formation (http://www.wun.ac.uk/wsc). Our hypothesis is that rates of biotic weathering are driven by the energy supply from plants to the organisms, controlling their biomass, surface area of contact with minerals and their capacity to interact chemically with minerals. Symbiotic fungal mycorrhiza of 90% of plant species are empowered with an available carbohydrate supply from plants that is unparalleled amongst soil microbes. They develop extensive mycelial networks that intimately contact minerals, which they weather aggressively. We hypothesise that mycorrhiza play a critical role through their focussing of photosynthate energy from plants into sub-surface weathering environments. Our work identifies how these fungal cells, and their secretions, interact with mineral surfaces and affect the rates of nutrient transfer from minerals to the organism. Investigating these living systems allows us to create new concepts and mathematical models that can describe biological weathering and be used in computer simulations of soil weathering dynamics. We are studying these biochemical interactions at 3 levels of observation: 1. At the molecular scale to understand interactions between living cells and minerals and to quantify the chemistry that breaks down the mineral structure; 2. At the soil grain scale to quantify the activity and spatial distribution of the fungi, roots and other organisms (e.g. bacteria) and their effects on the rates at which minerals are dissolved to release nutrients; 3. At soil profile scale to test models for the spatial distribution of active fungi and carbon energy and their seasonal variability and impact on mineral dissolution rates. Here we present early results from molecular and soil grain scale experiments. We have grown pure culture (Suillus bovinus, Paxillus involutus) mycorrhizal mycelial networks associated with pine trees in otherwise sterile (agar) and also non-sterile (peat) microcosms, which include mineral sections and powders of biotite, apatite and quartz. 14C labelling has been used to map C flux through the microcosms and to determine the transfer of photosynthate energy into the weathering arenas. We have used Vertical Scanning Interferometry (VSI) to assess volumetric alteration of mineral substrates in contact with fungi. Focused Ion Beam (FIB)- Transmission Electron Microscope (TEM) work provides evidence for increased mechanical forcing and possible alteration of biotite surfaces with greater fungi contact time. We also present real-time in situ observations of mineral-organic acid and mineral-exudate interactions using Atomic Force Microscopy (AFM).

Earthworms and priming of soil organic matter - The impact of food sources, food preferences and fauna - microbiota interactions

NASA Astrophysics Data System (ADS)

Potthoff, Martin; Wichern, Florian; Dyckmans, Jens; Joergensen, Rainer Georg

2016-04-01

Earthworms deeply interact with the processes of soil organic matter turnover in soil. Stabilization of carbon by soil aggregation and in the humus fraction of SOM are well known processes related to earthworm activity and burrowing. However, recent research on priming effects showed inconsistent effects for the impact of earthworm activity. Endogeic earthworms can induce apparent as well as true positive priming effects. The main finding is almost always that earthworm increase the CO2 production from soil. The sources of this carbon release can vary and seem to depend on a complex interaction of quantity and quality of available carbon sources including added substrates like straw or other compounds, food preferences and feeding behavior of earthworms, and soil properties. Referring to recent studies on earthworm effects on soil carbon storage and release (mainly Eck et al. 2015 Priming effects of Aporrectodea caliginosa on young rhizodeposits and old soil organic matter following wheat straw addition, European Journal of Soil Biology 70:38-45; Zareitalabad et al. 2010 Decomposition of 15N-labelled maize leaves in soil affected by endogeic geophagous Aporrectodea caliginosa, Soil Biology and Biochemistry 42(2):276-282; and Potthoff et al. 2001 Short-term effects of earthworm activity and straw amendment on the microbial C and N turnover in a remoistened arable soil after summer drought, Soil Biology and Biochemistry 33(4):583-591) we summaries the knowledge on earthworms and priming and come up with a conceptual approach and further research needs.

Soil conditions drive changes in a key leaf functional trait through environmental filtering and facilitative interactions

NASA Astrophysics Data System (ADS)

Molina-Venegas, Rafael; Aparicio, Abelardo; Lavergne, Sébastien; Arroyo, Juan

2018-01-01

Non-random patterns in the functional structure of communities are often interpreted as evidence for different forces governing their assemblage. However, community assembly processes may act antagonistically, countering each other's signatures on the functional structure of communities, which may lead to spurious inferences on the underlying mechanisms. To illustrate this issue, we assessed the joint effects of environmental filtering and facilitative interactions on a key leaf functional trait (i.e. specific leaf area, SLA) in Mediterranean dwarf-shrub communities, using a two-scale sampling approach. Specifically, we analyzed differences in community-weighted mean SLA values (CWM-SLA) between communities (community-scale) and between guilds within communities (guild-scale, i.e. individuals sampled in understorey, overstorey and open-ground conditions) across contrasted soil environments and elevational gradients. We found that communities on harsh edaphic conditions (i.e. dolomite habitats) showed significantly lower CWM-SLA values than communities on more fertile habitats. In contrast, elevation was a poor predictor of differences in CWM-SLA between the communities. This suggests that environmental filtering may influence leaf trait variation along soil gradients irrespective of elevation. On the other hand, communities on dolomite habitats showed strong differences in CWM-SLA between understorey (higher CWM-SLA) and either open-ground and overstorey guilds (lower CWM-SLA), whereas communities on more fertile soils showed no differences between the guilds. The strong differences in CWM-SLA between understorey and non-understorey guilds in dolomite communities suggest that facilitative interactions may be particularly at stake under stressful edaphic conditions, thus partially mitigating the effect of environmental filtering (i.e. low SLA values) on communities growing in harsh soils.

Surface interactions between gold nanoparticles and biochar

USDA-ARS?s Scientific Manuscript database

Engineered nanomaterials are directly applied to agricultural soils as a part of pesticide/fertilize formulations and sludge/manure amendments. Yet, no prior reports are available on the extent and reversibility of gold nanoparticles (nAu) retention by soil components including charcoal black carbo...

Effects of different regulatory methods on improvement of greenhouse saline soils, tomato quality, and yield.

PubMed

Maomao, Hou; Xiaohou, Shao; Yaming, Zhai

2014-01-01

To identify effective regulatory methods scheduling with the compromise between the soil desalination and the improvement of tomato quality and yield, a 3-year field experiment was conducted to evaluate and compare the effect of straw mulching and soil structure conditioner and water-retaining agent on greenhouse saline soils, tomato quality, and yield. A higher salt removing rate of 80.72% in plough layer with straw mulching was obtained based on the observation of salt mass fraction in 0 ~ 20 cm soil layer before and after the experiment. Salts were also found to move gradually to the deeper soil layer with time. Straw mulching enhanced the content of soil organic matter significantly and was conductive to reserve soil available N, P, and K, while available P and K in soils of plough layer with soil structure conditioner decreased obviously; thus a greater usage of P fertilizer and K fertilizer was needed when applying soil structure conditioner. Considering the evaluation indexes including tomato quality, yield, and desalination effects of different regulatory methods, straw mulching was recommended as the main regulatory method to improve greenhouse saline soils in south China. Soil structure conditioner was the suboptimal method, which could be applied in concert with straw mulching.

Performance of buried pipe installation.

DOT National Transportation Integrated Search

2010-05-01

The purpose of this study is to determine the effects of geometric and mechanical parameters : characterizing the soil structure interaction developed in a buried pipe installation located under : roads/highways. The drainage pipes or culverts instal...

Characterizing Wheel-Soil Interaction Loads Using Meshfree Finite Element Methods: A Sensitivity Analysis for Design Trade Studies

NASA Technical Reports Server (NTRS)

Contreras, Michael T.; Trease, Brian P.; Bojanowski, Cezary; Kulakx, Ronald F.

2013-01-01

A wheel experiencing sinkage and slippage events poses a high risk to planetary rover missions as evidenced by the mobility challenges endured by the Mars Exploration Rover (MER) project. Current wheel design practice utilizes loads derived from a series of events in the life cycle of the rover which do not include (1) failure metrics related to wheel sinkage and slippage and (2) performance trade-offs based on grouser placement/orientation. Wheel designs are rigorously tested experimentally through a variety of drive scenarios and simulated soil environments; however, a robust simulation capability is still in development due to myriad of complex interaction phenomena that contribute to wheel sinkage and slippage conditions such as soil composition, large deformation soil behavior, wheel geometry, nonlinear contact forces, terrain irregularity, etc. For the purposes of modeling wheel sinkage and slippage at an engineering scale, meshfree nite element approaches enable simulations that capture su cient detail of wheel-soil interaction while remaining computationally feasible. This study implements the JPL wheel-soil benchmark problem in the commercial code environment utilizing the large deformation modeling capability of Smooth Particle Hydrodynamics (SPH) meshfree methods. The nominal, benchmark wheel-soil interaction model that produces numerically stable and physically realistic results is presented and simulations are shown for both wheel traverse and wheel sinkage cases. A sensitivity analysis developing the capability and framework for future ight applications is conducted to illustrate the importance of perturbations to critical material properties and parameters. Implementation of the proposed soil-wheel interaction simulation capability and associated sensitivity framework has the potential to reduce experimentation cost and improve the early stage wheel design proce

Vibration Based Wind Turbine Tower Foundation Design Utilizing Soil-Foundation-Structure Interaction

NASA Astrophysics Data System (ADS)

Al Satari, P. E. Mohamed; Hussain, S. E. Saif

2008-07-01

Wind turbines have been used to generate electricity as an alternative energy source to conventional fossil fuels. This case study is for multiple wind towers located at different villages in Alaska where severe arctic weather conditions exist. The towers are supported by two different types of foundations; large mat or deep piles foundations. Initially, a Reinforced Concrete (RC) mat foundation was utilized to provide the system with vertical and lateral support. Where soil conditions required it, a pile foundation solution was devised utilizing a 30″ thick RC mat containing an embedded steel grillage of W18 beams supported by 20″-24″ grouted or un-grouted piles. The mixing and casting of concrete in-situ has become the major source of cost and difficulty of construction at these remote Alaska sites. An all-steel foundation was proposed for faster installation and lower cost, but was found to impact the natural frequencies of the structural system by significantly softening the foundation system. The tower-foundation support structure thus became near-resonant with the operational frequencies of the wind turbine leading to a likelihood of structural instability or even collapse. A detailed 3D Finite-Element model of the original tower-foundation-pile system with RC foundation was created using SAP2000. Soil springs were included in the model based on soil properties obtained from the geotechnical consultant. The natural frequency from the model was verified against the tower manufacturer analytical and the experimental values. Where piles were used, numerous iterations were carried out to eliminate the need for the RC and optimize the design. An optimized design was achieved with enough separation between the natural and operational frequencies to prevent damage to the structural system eliminating the need for any RC encasement to the steel foundation or grouting to the piles.

Sequestration of Carbon in Mycorrhizal Fungi Under Nitrogen Fertilization

NASA Astrophysics Data System (ADS)

Treseder, K. K.; Turner, K. M.

2005-12-01

Mycorrhizal fungi are root symbionts that facilitate plant uptake of soil nutrients in exchange for plant carbohydrates. They grow in almost every terrestrial ecosystem on earth, form relationships with about 80% of plant species, and receive 10 to 20% of the carbon fixed by their host plants. As such, they could potentially sequester a significant amount of carbon in ecosystems. We hypothesized that nitrogen fertilization would decrease carbon storage in mycorrhizal fungi, because plants should reduce investment of carbon in mycorrhizal fungi when nitrogen availability is high. We measured the abundance of two major groups of mycorrhizal fungi, arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi, in control and nitrogen-fertilized plots within three boreal ecosystems of inland Alaska. The ecosystems represented different recovery stages following severe fire, and comprised a young site dominated by AM fungi, an old site dominated by ECM fungi, and an intermediate site co-dominated by both groups. Pools of mycorrhizal carbon included root-associated AM and ECM structures, soil-associated AM hyphae, and soil-associated glomalin. Glomalin is a glycoprotein produced only by AM fungi. It is present in the cell walls of AM hyphae, and then is deposited in the soil as the hyphae senesce. Nitrogen significantly altered total mycorrhizal carbon pools, but its effect varied by site (site * N interaction, P = 0.05). Under nitrogen fertilization, mycorrhizal carbon was reduced from 99 to 50 g C m2 in the youngest site, was increased from 124 to 203 g C m2 in the intermediate-aged site, and remained at 35 g C m2 in the oldest site. The changes in total mycorrhizal carbon stocks were driven mostly by changes in glomalin (site * N interaction, P = 0.05), and glomalin stocks were strongly correlated with AM hyphal abundance (P < 0.01). Nevertheless, it is not clear why AM hyphae responded differently to nitrogen fertilization in the different sites. Carbon stocks within root-associated AM structures increased significantly with nitrogen fertilization across all sites (P = 0.001), as did root-associated ECM structures (P = 0.021). The amount of carbon sequestered within living mycorrhizal structures (0.013 to 0.21 g m2), however, was modest compared to that of glomalin (91 g m2). We conclude that allocation by AM fungi to hyphal growth influenced the size of glomalin stocks in the soil, and that nitrogen fertilization altered investment in hyphal growth, with potential consequences for soil carbon storage. However, the nitrogen response was inconsistent among boreal forest ecosystems. An understanding of the mechanisms underlying this variation would improve our ability to predict ecosystem feedbacks to global change.

Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

PubMed

Zhang, Cui-Jing; Delgado-Baquerizo, Manuel; Drake, John E; Reich, Peter B; Tjoelker, Mark G; Tissue, David T; Wang, Jun-Tao; He, Ji-Zheng; Singh, Brajesh K

2018-04-01

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Morphological Adaptations for Digging and Climate-Impacted Soil Properties Define Pocket Gopher (Thomomys spp.) Distributions

PubMed Central

Marcy, Ariel E.; Fendorf, Scott; Patton, James L.; Hadly, Elizabeth A.

2013-01-01

Species ranges are mediated by physiology, environmental factors, and competition with other organisms. The allopatric distribution of five species of northern Californian pocket gophers (Thomomys spp.) is hypothesized to result from competitive exclusion. The five species in this environmentally heterogeneous region separate into two subgenera, Thomomys or Megascapheus, which have divergent digging styles. While all pocket gophers dig with their claws, the tooth-digging adaptations of subgenus Megascapheus allow access to harder soils and climate-protected depths. In a Northern Californian locality, replacement of subgenus Thomomys with subgenus Megascapheus occurred gradually during the Pleistocene-Holocene transition. Concurrent climate change over this transition suggests that environmental factors – in addition to soil – define pocket gopher distributional limits. Here we show 1) that all pocket gophers occupy the subset of less energetically costly soils and 2) that subgenera sort by percent soil clay, bulk density, and shrink-swell capacity (a mineralogical attribute). While clay and bulk density (without major perturbations) stay constant over decades to millennia, low precipitation and high temperatures can cause shrink-swell clays to crack and harden within days. The strong yet underappreciated interaction between soil and moisture on the distribution of vertebrates is rarely considered when projecting species responses to climatic change. Furthermore, increased precipitation alters the weathering processes that create shrink-swell minerals. Two projected outcomes of ongoing climate change—higher temperatures and precipitation—will dramatically impact hardness of soil with shrink-swell minerals. Current climate models do not include factors controlling soil hardness, despite its impact on all organisms that depend on a stable soil structure. PMID:23717675

Crystal structure control of aluminized clay minerals on the mobility of caesium in contaminated soil environments

NASA Astrophysics Data System (ADS)

Dzene, Liva; Ferrage, Eric; Viennet, Jean-Christophe; Tertre, Emmanuel; Hubert, Fabien

2017-02-01

Radioactive caesium pollution resulting from Fukushima Dai-ichi and Chernobyl nuclear plant accidents involves strong interactions between Cs+ and clays, especially vermiculite-type minerals. In acidic soil environments, such as in Fukushima area, vermiculite is subjected to weathering processes, resulting in aluminization. The crystal structure of aluminized clays and its implications for Cs+ mobility in soils remain poorly understood due to the mixture of these minerals with other clays and organic matter. We performed acidic weathering of a vermiculite to mimic the aluminization process in soils. Combination of structure analysis and Cs+ extractability measurements show that the increase of aluminization is accompanied by an increase in Cs+ mobility. Crystal structure model for aluminized vermiculite is based on the interstratification of unaltered vermiculite layers and aluminized layers within the same particle. Cs+ in vermiculite layers is poorly mobile, while the extractability of Cs+ is greatly enhanced in aluminized layers. The overall reactivity of the weathered clay (cation exchange capacity, Cs+ mobility) is then governed by the relative abundance of the two types of layers. The proposed layer model for aluminized vermiculite with two coexisting populations of caesium is of prime importance for predicting the fate of caesium in contaminated soil environments.

Multi-scale sensitivity analysis of pile installation using DEM

NASA Astrophysics Data System (ADS)

Esposito, Ricardo Gurevitz; Velloso, Raquel Quadros; , Eurípedes do Amaral Vargas, Jr.; Danziger, Bernadete Ragoni

2017-12-01

The disturbances experienced by the soil due to the pile installation and dynamic soil-structure interaction still present major challenges to foundation engineers. These phenomena exhibit complex behaviors, difficult to measure in physical tests and to reproduce in numerical models. Due to the simplified approach used by the discrete element method (DEM) to simulate large deformations and nonlinear stress-dilatancy behavior of granular soils, the DEM consists of an excellent tool to investigate these processes. This study presents a sensitivity analysis of the effects of introducing a single pile using the PFC2D software developed by Itasca Co. The different scales investigated in these simulations include point and shaft resistance, alterations in porosity and stress fields and particles displacement. Several simulations were conducted in order to investigate the effects of different numerical approaches showing indications that the method of installation and particle rotation could influence greatly in the conditions around the numerical pile. Minor effects were also noted due to change in penetration velocity and pile-soil friction. The difference in behavior of a moving and a stationary pile shows good qualitative agreement with previous experimental results indicating the necessity of realizing a force equilibrium process prior to any load-test to be simulated.

Stabilization of heavy metals in soil using two organo-bentonites.

PubMed

Yu, Kai; Xu, Jian; Jiang, Xiaohong; Liu, Cun; McCall, Wesley; Lu, Jinlong

2017-10-01

Stabilization of Cu, Zn, Cd, Hg, Cr and As in soil using tetramethylammonium (TMA) and dodecyltrimethylammonium (DTMA) modified bentonites (T-Bents and D-Bents) as amendments was investigated. Toxicity characteristic leaching procedure (TCLP) was used to quantify the metal mobility after soil treatment. The structural parameters of modified bentonites, including the BET surface area, basal spacing and zeta potential were obtained as a function of the TMA and DTMA loading at 40, 80, 120, 160 and 200% of the bentonite's cation exchange capacity, respectively. The results indicated that the characteristics of the organo-bentonites fundamentally varied depending on the species and concentration of modifiers loaded on bentonite. T-Bents and D-Bents manifested distinct immobilization effectiveness towards various metals. In association with the organo-bentonite characteristics, the main interactive mechanisms for Cu, Zn and Cd proceeded via cation exchange, Hg proceeded via physical adsorption and partitioning, Cr and As proceeded via specific adsorption and electrostatic attraction, respectively. This study provided operational and mechanistic basis for optimizing the organic clay synthesis and selecting as the appropriate amendment for remediation of heavy metal contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multi-scale sensitivity analysis of pile installation using DEM

NASA Astrophysics Data System (ADS)

Esposito, Ricardo Gurevitz; Velloso, Raquel Quadros; , Eurípedes do Amaral Vargas, Jr.; Danziger, Bernadete Ragoni

2018-07-01

The disturbances experienced by the soil due to the pile installation and dynamic soil-structure interaction still present major challenges to foundation engineers. These phenomena exhibit complex behaviors, difficult to measure in physical tests and to reproduce in numerical models. Due to the simplified approach used by the discrete element method (DEM) to simulate large deformations and nonlinear stress-dilatancy behavior of granular soils, the DEM consists of an excellent tool to investigate these processes. This study presents a sensitivity analysis of the effects of introducing a single pile using the PFC2D software developed by Itasca Co. The different scales investigated in these simulations include point and shaft resistance, alterations in porosity and stress fields and particles displacement. Several simulations were conducted in order to investigate the effects of different numerical approaches showing indications that the method of installation and particle rotation could influence greatly in the conditions around the numerical pile. Minor effects were also noted due to change in penetration velocity and pile-soil friction. The difference in behavior of a moving and a stationary pile shows good qualitative agreement with previous experimental results indicating the necessity of realizing a force equilibrium process prior to any load-test to be simulated.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

PubMed

Pérez-Valera, Eduardo; Goberna, Marta; Faust, Karoline; Raes, Jeroen; García, Carlos; Verdú, Miguel

2017-01-01

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Soils as Sediment database: closing a gap between soil science and geomorphology

NASA Astrophysics Data System (ADS)

Kuhn, Nikolaus J.

2016-04-01

Soils are an interface between the Earth's spheres and shaped by the nature of the interaction between them. The relevance of soil properties for the nature of the interaction between atmosphere, hydrosphere and biosphere is well-studied and accepted, on point- or ecotone-scale. However, this understanding of the largely vertical connections between spheres is not matched by a similar recognition of soil properties affecting processes acting largely in a lateral way across the land surface, such as erosion, transport and deposition of soil. Key areas where such an understanding is essential are all issues related to the lateral movement of soil-bound substances that affect the nature of soils itself, as well as water or vegetation downslope from the source area. The redistribution of eroded soil falls several disciplines, most notably soil science, agronomy, hydrology and geomorphology. Accordingly, the way sediment is described differs: in soil science, aggregation and structure are essential properties, while most process-based soil erosion models treat soil as a mixture of individual mineral grains, based on concepts derived in fluvial geomorphology or civil engineering. The actual behavior of aggregated sediment is not reflected by either approach and difficult to capture due to the dynamic nature of aggregation, especially in an environment such as running water. Still, a proxy to assess the uncertainties introduced by aggregation on the behavior of soil as sediment would represent a step forward. To develop such a proxy, a database collating relevant soil and sediment properties could serve as an initial step to identify which soil types and erosion scenarios are prone to generate a high uncertainty compared to the use of soil texture in erosion models. Furthermore, it could serve to develop standardized analytical procedures for appropriate description of soil as sediment.

Reinforced soil structures. Volume I. Design and construction guidelines

DOT National Transportation Integrated Search

1990-11-01

This report presents comprehensive guidelines for evaluating and using soil reinforcement techniques in the construction of retaining walls, embankment slopes, and natural or cut slopes. A variety of available systems for reinforced soil including in...

Reinforced soil structures. Volume I, Design and construction guidelines

DOT National Transportation Integrated Search

1990-11-01

This report presents comprehensive guidelines for evaluating and using soil reinforcement techniques in the construction of retaining walls, embankment slopes, and natural or cut slopes. A variety of available systems for reinforced soil including in...

Effect of Metal Oxide Nanoparticles on Microbial Community Structure and Function in Two Different Soil Types

PubMed Central

Frenk, Sammy; Ben-Moshe, Tal; Dror, Ishai; Berkowitz, Brian; Minz, Dror

2013-01-01

Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe3O4) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe3O4 changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity. PMID:24349575

Assembly of the outermost spore layer: pieces of the puzzle are coming together.

PubMed

Stewart, George C

2017-05-01

Certain endospore-forming soil dwelling bacteria are important human, animal or insect pathogens. These organisms produce spores containing an outer layer, the exosporium. The exosporium is the site of interactions between the spore and the soil environment and between the spore and the infected host during the initial stages of infection. The composition and assembly process of the exosporium are poorly understood. This is partly due to the extreme stability of the exosporium that has proven to be refractive to existing methods to deconstruct the intact structure into its component parts. Although more than 20 proteins have been identified as exosporium-associated, their abundance, relationship to other proteins and the processes by which they are assembled to create the exosporium are largely unknown. In this issue of Molecular Microbiology, Terry, Jiang, and colleagues in Per Bullough's laboratory show that the ExsY protein is a major structural protein of the exosporium basal layer of B. cereus family spores and that it can self-assemble into complex structures that possess many of the structural features characteristic of the exosporium basal layer. The authors refined a model for exosporium assembly. Their findings may have implications for exosporium formation in other spore forming bacteria, including Clostridium species. © 2017 John Wiley & Sons Ltd.

Development and Verification of the Soil-Pile Interaction Extension for SubDyn

DOE Office of Scientific and Technical Information (OSTI.GOV)

Damiani, Rick R; Wendt, Fabian F

SubDyn is the substructure structural-dynamics module for the aero-hydro-servo-elastic tool FAST v8. SubDyn uses a finite-element model (FEM) to simulate complex multimember lattice structures connected to conventional turbines and towers, and it can make use of the Craig-Bampton model reduction. Here we describe the newly added capability to handle soil-pile stiffness and compare results for monopile and jacket-based offshore wind turbines as obtained with FAST v8, SACS, and EDP (the latter two are modeling software packages commonly used in the offshore oil and gas industry). The level of agreement in terms of modal properties and loads for the entire offshoremore » wind turbine components is excellent, thus allowing SubDyn and FAST v8 to accurately simulate offshore wind turbines on fixed-bottom structures and accounting for the effect of soil dynamics, thus reducing risk to the project.« less

Biophysical landscape interactions: Bridging disciplines and scale with connectivity

NASA Astrophysics Data System (ADS)

van der Ploeg, Martine; Baartman, Jantiene; Robinson, David

2017-04-01

The combination of climate change, population growth and soil threats, such as carbon loss, biodiversity decline or erosion amongst others , increasingly confront the global community [1]. One of the major challenges in studying processes involved in soil threats, landscape resilience, ecosystem stability, sustainable land management and the economic consequences, is that it is an interdisciplinary field [2], that needs less stringent scientific disciplinary boundaries [3]. As a result of disciplinary focus, ambiguity may arise on the understanding of landscape interactions, and this is especially true in the interaction between a landscape's physical and biological processes [4]. Another important aspect in biophysical landscape interactions are the differences in scale related to the various processes that play a role in these systems. While scaling of environmental processes is possible, as long as the phenomena at hand can be described by the same set of differential equations [5], biophysical landscape interactions pose problems for scaling approaches. Landscape position and land use impact the coupled processes in soil and vegetation. Differences in micro-behavior, driven by the interplay of heterogeneous soil and vegetation dynamics, impact emergent characteristics across a landscape. A complicating factor is the response of vegetation to changing environmental conditions, including a possible and often unknown time-lag. By altering soil conditions, plants may leave an imprint in the landscape that remains even after vegetation has disappeared due to e.g. drought, wildfire or overgrazing. Plants also respond biochemically to their environment, while the models used for hydrology are often based on physical interactions. Gene-expression and genotype adaptation may further complicate our modelling efforts in for example climate change impacts. What are we missing by not having more connectivity in our thinking, and what we can solve? We think that integrated concepts of biophysical landscape interactions are needed to evaluate soil water availability in relation to the stability of natural vegetation, especially in the perspective of soil threats, population growth, climate change, and global water scarcity. An integrated concept can only be established by bridging the gap between several disciplines, but needs to be appealing to those disciplines at the same time. As evidence suggests interdisciplinary work is more challenging to get funded [6]. The key aspect of the connectivity concept is that it can create pathways for feedbacks which are so often missing in soil and water models. Connectivity could thus play an important role in bridging disciplines and scales. [1] Schwilch G, Bernet L. Fleskens L, Giannakis E, Leventon J, Marañón T, Mills J, Short C, Stolte J, van Delden H, Verzandvoort S. 2016. Operationalizing ecosystem services for the mitigation of soil threats: A proposed framework. Ecological Indicators 67: 586-597,doi:10.1016/j.ecolind.2016.03.016 [2] Pelletier JD, DeLong SB, Orem CA, Becerra P, Compton K, Gressett K, Lyons-Baral J, McGuire LA, Molaro JL, Spinler JCCF. 2012. How do vegetation bands form in dry lands? Insights from numerical modeling and field studies in southern Nevada, USA. Journal of Geophysical Research: Earth Surface 117: F04026,doi:10.1029/2012JF002465 [3] Liu J, Dietz T, Carpenter SR, Alberti M, Folke C, Moran E, ..., Ostrom E. 2007. Complexity of coupled human and natural systems. Science 317.5844: 1513-1516,doi:10.1126/science.1144004 [4] Cook BJ, Hauer FR. 2007. Effects of hydrologic connectivity on water chemistry, soils, and vegetation structure and function in an intermontane depressional wetland landscape. Wetlands 27.3: 719-738,doi:10.1672/0277-5212(2007)27 [5] Roth K. 2008. Scaling of water flow through porous media and soils. European journal of soil science, 59(1), 125-130, doi: 10.1111/j.1365-2389.2007.00986.x [6] Bromham, L, Dinnage R, Hua X. 2016. Interdisciplinary research has consistently lower funding success. Nature 534: 684-687,doi:10.1038/nature18315

Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs

PubMed Central

Stacheter, Astrid; Noll, Matthias; Lee, Charles K; Selzer, Mirjam; Glowik, Beate; Ebertsch, Linda; Mertel, Ralf; Schulz, Daria; Lampert, Niclas; Drake, Harold L; Kolb, Steffen

2013-01-01

The role of soil methylotrophs in methanol exchange with the atmosphere has been widely overlooked. Methanol can be derived from plant polymers and be consumed by soil microbial communities. In the current study, methanol-utilizing methylotrophs of 14 aerated soils were examined to resolve their comparative diversities and capacities to utilize ambient concentrations of methanol. Abundances of cultivable methylotrophs ranged from 106–108 gsoilDW−1. Methanol dissimilation was measured based on conversion of supplemented 14C-methanol, and occurred at concentrations down to 0.002 μmol methanol gsoilDW−1. Tested soils exhibited specific affinities to methanol (a0s=0.01 d−1) that were similar to those of other environments suggesting that methylotrophs with similar affinities were present. Two deep-branching alphaproteobacterial genotypes of mch responded to the addition of ambient concentrations of methanol (⩽0.6 μmol methanol gsoilDW−1) in one of these soils. Methylotroph community structures were assessed by amplicon pyrosequencing of genes of mono carbon metabolism (mxaF, mch and fae). Alphaproteobacteria-affiliated genotypes were predominant in all investigated soils, and the occurrence of novel genotypes indicated a hitherto unveiled diversity of methylotrophs. Correlations between vegetation type, soil pH and methylotroph community structure suggested that plant–methylotroph interactions were determinative for soil methylotrophs. PMID:23254514

The interactive effects of fire and diversity on short-term responses of ecosystem processes in experimental mediterranean grasslands.

PubMed

Dimitrakopoulos, Panayiotis G; Siamantziouras, Akis-Stavros D; Galanidis, Alexandros; Mprezetou, Irene; Troumbis, Andreas Y

2006-06-01

We conducted a field experiment using constructed communities to test whether species richness contributed to the maintenance of ecosystem processes under fire disturbance. We studied the effects of diversity components (i.e., species richness and species composition) upon productivity, structural traits of vegetation, decomposition rates, and soil nutrients between burnt and unburnt experimental Mediterranean grassland communities. Our results demonstrated that fire and species richness had interactive effects on aboveground biomass production and canopy structure components. Fire increased biomass production of the highest-richness communities. The effects of fire on aboveground biomass production at different levels of species richness were derived from changes in both vertical and horizontal canopy structure of the communities. The most species-rich communities appeared to be more resistant to fire in relation to species-poor ones, due to both compositional and richness effects. Interactive effects of fire and species richness were not important for belowground processes. Decomposition rates increased with species richness, related in part to increased levels of canopy structure traits. Fire increased soil nutrients and long-term decomposition rate. Our results provide evidence that composition within richness levels had often larger effects on the stability of aboveground ecosystem processes in the face of fire disturbance than species richness per se.

Effects of soil and space on the woody species composition and vegetation structure of three Cerrado phytophysiognomies in the Cerrado-Amazon transition.

PubMed

Maracahipes-Santos, L; Lenza, E; Santos, J O; Mews, H A; Oliveira, B

2017-11-01

The Cerrado Biome is considered one of the world's biodiversity hotspots because of its rich biodiversity, the high level of endemism and the increasing threat. The Cerrado is composed by a mosaic of different vegetation types, including physiognomies that vary from grasslands (campo limpo) to savannas (typical cerrado or cerrado sensu stricto) and cerrado woodlands (cerradão). However, the factors that determine the composition of the Cerrado's flora and the structure of the physiognomies that compose this biome are still poorly understood. Here, we investigate the influence of the chemical and granulometric properties of the soil and the effect of geographic distance on the occurrence and abundance of woody species in three Cerrado phytophysiognomies - cerrado woodland (cerradão), dense cerrado savanna and typical cerrado savanna - in the Cerrado-Amazon transition. We tested the hypothesis that the edaphic characteristics and geographic space determine the species composition and the structure of the woody vegetation of these three phytophysiognomies. We demonstrate that the dissimilarities in the structure and composition of the three sites were determined more by space (13% of explanation) than edaphic properties (1%), but primarily by the interaction between these two factors (26%). We conclude that, in situations where the chemical and granulometric properties of the soil are relatively homogeneous, as we found in the present study, geographic distance between sites has a greater influence than variation in the substrate's properties on modelling the occurrence and abundance of the woody plant species in the Cerrado.

Interaction effects of As, Cd and Pb on their respective bioaccessibility with time in co-contaminated soils assessed by the Unified BARGE Method.

PubMed

Xia, Qing; Lamb, Dane; Peng, Cheng; Ng, Jack C

2017-02-01

Interaction effects of As, Cd and Pb on their respective bioaccessibility in co-contaminated soils were reported. In addition, the influence of aging time (up to 90 days) on potential interactions was also investigated. Experiments were carried out by spiking four diverse soils with single, binary or ternary mixtures of As, Cd and Pb. Soils were measured for bioaccessibility at different aging periods. Results demonstrate that bioaccessibility of As, Cd and Pb reached a steady state after soils were aged for 30 days. Bioaccessibility of As, Cd and Pb in soils spiked with binary mixtures of As, Cd and Pb were not affected by the other co-existing metal/metalloid. But when As, Cd and Pb were introduced together to acidic soils which lacked abundant binding sites, intestinal bioaccessibility of Cd was increased at the early stage of aging (7 to 30 days) whilst bioaccessibility of As and Pb remained unchanged. However, when Pb and As were added after Cd has been incubated in soil for 7 days, Cd intestinal bioaccessibility was not influenced by As and Pb. Therefore, a number of factors should be taken into consideration when estimating the bioaccessibility of mixed As, Cd and Pb, including the loadings of As, Cd and Pb in soils, the time for which they have been aged together and the time period between As, Cd and Pb entering the soils.

Assessment of trace heavy metals dynamics during the interaction of aqueous solutions with the artificial OECD soil: Evaluation of the effect of soil organic matter content and colloidal mobilization.

PubMed

Pontoni, Ludovico; van Hullebusch, Eric D; Fabbricino, Massimiliano; Esposito, Giovanni; Pirozzi, Francesco

2016-11-01

A micro-contamination phenomenon was reproduced and studied at lab-scale, mimicking the irrigation of a standard artificial soil with a water solution containing three Heavy Metals (HMs) at trace concentration level. To assess the dynamics of micro-pollutants accumulation and migration trough the soil, the organic matter in the soil was varied, together with sodicity of the irrigation water. Accumulation of the investigated contaminants was observed mainly in the top layer (≤1 cm) of the irrigated soil. This was attributed to the high interaction capacity of the soil compared to the low HM concentrations in the water phase. HMs transport pattern was described assuming a multi-component mechanism including: i) the interaction of HMs with the colloidal phase of the soil; ii) the slow and constant release of small molecular weight ligands detaching from the soil immobile matrix; iii) the transportation of HMs through the soil by these low molecular weight chaperon molecules. The mobility was directly related to the soil organic matter (SOM), since higher amount of SOM correspond to a higher number of chaperon molecules. In the first centimetre of the soil the metals were mostly bound to the acid labile fraction. Very low mobilization was observed with increasing sodicity in the leaching water, since such conditions were unfavourable to the colloidal mobilization of SOM. This indicated that water/soil transfer of pollutant is not only related to the contaminant concentration in the irrigation water but also to the characteristics of the aqueous solution and to the physical-chemical properties of the soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Bacterial mycophagy: definition and diagnosis of a unique bacterial-fungal interaction.

PubMed

Leveau, Johan H J; Preston, Gail M

2008-01-01

This review analyses the phenomenon of bacterial mycophagy, which we define as a set of phenotypic behaviours that enable bacteria to obtain nutrients from living fungi and thus allow the conversion of fungal into bacterial biomass. We recognize three types of bacterial strategies to derive nutrition from fungi: necrotrophy, extracellular biotrophy and endocellular biotrophy. Each is characterized by a set of uniquely sequential and differently overlapping interactions with the fungal target. We offer a detailed analysis of the nature of these interactions, as well as a comprehensive overview of methodologies for assessing and quantifying their individual contributions to the mycophagy phenotype. Furthermore, we discuss future prospects for the study and exploitation of bacterial mycophagy, including the need for appropriate tools to detect bacterial mycophagy in situ in order to be able to understand, predict and possibly manipulate the way in which mycophagous bacteria affect fungal activity, turnover, and community structure in soils and other ecosystems.

Significance of wall structure, macromolecular composition, and surface polymers to the survival and transport of Cryptosporidium parvum Oocysts

USDA-ARS?s Scientific Manuscript database

The structure and composition of the oocyst wall are primary factors determining the survival of Cryptosporidium parvum oocysts outside the host. An external polymer matrix (glycocalyx) may mediate interactions with environmental surfaces and, thus, affect the transport of oocysts in water, soil, an...

Performance evaluation of buried pipe installation.

DOT National Transportation Integrated Search

2010-05-01

The purpose of this study is to determine the effects of geometric and mechanical parameters characterizing the soil structure interaction developed in a buried pipe installation located under roads/highways. The drainage pipes or culverts installed ...

Field study of integral backwall with elastic inclusion.

DOT National Transportation Integrated Search

2005-01-01

Jointless construction is considered an effective design option to reduce bridge maintenance costs and resist seismic loads. Although these attributes make the integral bridge an increasingly popular choice, soil-structure interaction issues unique t...

Exploring functional relationships between post-fire soil water repellency, soil structure and physico-chemical properties

NASA Astrophysics Data System (ADS)

Quarfeld, Jamie; Brook, Anna; Keestra, Saskia; Wittenberg, Lea

2016-04-01

Soil water repellency (WR) and aggregate stability (AS) are two soil properties that are typically modified after burning and impose significant influence on subsequent hydrological and geomorphological dynamics. The response of AS and soil WR to fire depends upon how fire has influenced other key soil properties (e.g. soil OM, mineralogy). Meanwhile, routine thinning of trees and woody vegetation may alter soil properties (e.g. structure and porosity, wettability) by use of heavy machinery and species selection. The study area is situated along a north-facing slope of Mount Carmel national park (Israel). The selected sites are presented as a continuum of management intensity and fire histories. To date, the natural baseline of soil WR has yet to be thoroughly assessed and must be investigated alongside associated soil aggregating parameters in order to understand its overall impact. This study examines (i) the natural baseline of soil WR and physical properties compared to those of disturbed sites in the immediate (controlled burn) and long-term (10-years), and (ii) the interactions of soil properties with different control factors (management, surface cover, seasonal-temporal, burn temperature, soil organic carbon (OC) and mineralogy) in Mediterranean calcareous soils. Analysis of surface soil samples before and after destruction of WR by heating (200-600°C) was implemented using a combination of traditional methods and infrared (IR) spectroscopy. Management and surface cover type conditioned the wettability, soil structure and porosity of soils in the field, although this largely did not affect the heat-induced changes observed in the lab. A positive correlation was observed along an increasing temperature gradient, with relative maxima of MWD and BD reached by most soils at the threshold of 400-500°C. Preliminary analyses of soil OC (MIR) and mineralogical composition (VIS-NIR) support existing research regarding: (i) the importance of soil OC quality and composition in determining wettability rather than quantity, as evidenced both by the high variation observed in the field and the strong presence of aliphatic functional groups in the absence of WR; and (ii) commonly proposed mechanisms affecting soil aggregate properties - albeit with differing temperature thresholds and longer exposure times employed in this study. Namely, these mechanisms tend to involve: (i) soil OM and WR reduction at low to moderate temperatures, and (ii) thermal fusion of particles within moderate to high temperatures. Overall, results suggest a positive influence of management on soil properties as well as high soil resilience to moderate severity fire disturbance in the studied areas. However, the specific changes in soil OM and mineral composition that are responsible for destruction of WR and subsequent changes in AS remain poorly understood. Based on these results, a key next step within this study will entail a closer examination of OC ratios and their potential links with certain mineral species known to influence soil aggregation and soil WR. Noting the importance of soil OM-mineralogical interactions on run-off and erosion processes, results may contribute to better prediction of post-fire responses in the future and improve the ability to fine-tune site specific management approaches accordingly.

Modeling Bacteria-Water Interactions in Soil: EPS Dynamics Under Evaporative Conditions

NASA Astrophysics Data System (ADS)

Furrer, J.; Hinestroza, H. F.; Guo, Y. S.; Gage, D. J.; Cho, Y. K.; Shor, L. M.

2017-12-01

The soil habitat represents a major linkage between the water and carbon cycles: the ability of soils to sequester or release carbon is determined primarily by soil moisture. Water retention and distribution in soils controls the abundance and activity of soil microbes. Microbes in turn impact water retention by creating biofilms, composed of extracellular polymeric substances (EPS). We model the effects of bacterial EPS on water retention at the pore scale. We use the lattice Boltzmann method (LBM), a well-established fluid dynamics modeling platform, and modify it to include the effects of water uptake and release by the swelling/shrinking EPS phase. The LB model is implemented in 2-D, with a non-ideal gas equation of state that allows condensation and evaporation of fluid in pore spaces. Soil particles are modeled according to experimentally determined particle size distributions and include realistic pore geometries, in contrast to many soil models which use spherical soil particles for simplicity. Model results are compared with evaporation experiments in soil micromodels and other simpler experimental systems, and model parameters are tuned to match experimental results. Drying behavior and solid-gel contact angle of EPS produced by the soil bacteria Sinorhizobium meliloti has been characterized and compared to the behavior of deionized water under the same conditions. The difference in behavior between the fluids is used to parameterize the model. The model shows excellent qualitative agreement for soil micromodels with both aggregated and non-aggregated particle arrangements under no-EPS conditions, and reproduces realistic drying behavior for EPS. This work represents a multi-disciplinary approach to understanding microbe-soil interactions at the pore scale.

Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species.

PubMed

Meiners, Scott J; Phipps, Kelsey K; Pendergast, Thomas H; Canam, Thomas; Carson, Walter P

2017-04-01

While both plant-soil feedbacks and allelochemical interactions are key drivers of plant community dynamics, the potential for these two drivers to interact with each other remains largely unexplored. If soil microbes influence allelochemical production, this would represent a novel dimension of heterogeneity in plant-soil feedbacks. To explore the linkage between soil microbial communities and plant chemistry, we experimentally generated soil microbial communities and evaluated their impact on leaf chemical composition and allelopathic potential. Four native perennial old-field species (two each of Aster and Solidago) were grown in pairwise combination with each species' soil microbial community as well as a sterilized inoculum. We demonstrated unequivocally that variation in soil microbial communities altered leaf chemical fingerprints for all focal plant species and also changed their allelopathic potential. Soil microbes reduced allelopathic potential in bioassays by increasing germination 25-54% relative to sterile control soils in all four species. Plants grown with their own microbial communities had the lowest allelopathic potential, suggesting that allelochemical production may be lessened when growing with microbes from conspecifics. The allelopathic potential of plants grown in congener and confamilial soils was indistinguishable from each other, indicating an equivalent response to all non-conspecific microbial communities within these closely related genera. Our results clearly demonstrated that soil microbial communities cause changes in leaf tissue chemistry that altered their allelopathic properties. These findings represent a new mechanism of plant-soil feedbacks that may structure perennial plant communities over very small spatial scales that must be explored in much more detail.

Effect of aggregation on SOC transport: linking soil properties to sediment organic matter

NASA Astrophysics Data System (ADS)

Kuhn, Nikolaus J.

2016-04-01

Soils are an interface between the Earth's spheres and shaped by the nature of the interaction between them. The relevance of soil properties for the nature of the interaction between atmosphere, hydrosphere and biosphere is well-studied and accepted, on point- or ecotone-scale. However, this understanding of the largely vertical connections between spheres is not matched by a similar recognition of soil properties affecting processes acting largely in a lateral way across the land surface, such as erosion, transport and deposition of soil and the associated organic matter. Understanding the redistribution of eroded soil organic matter falls into several disciplines, most notably soil science, agronomy, hydrology and geomorphology, and recently into biogeochemistry. Accordingly, the way soil and sediment are described differs: in soil science, aggregation and structure are essential properties, while most process-based soil erosion models treat soil as a mixture of individual mineral grains, based on concepts derived in fluvial geomorphology or civil engineering. The actual behavior of aggregated sediment and the associated organic matter is not reflected by either approach and difficult to capture due to the dynamic nature of aggregation, especially in an environment such as running water. Still, a proxy to assess the uncertainties introduced by aggregation on the behavior of soil/sediment organic while moving in water across landscapes and into the aquatic system would represent a major step forward. To develop such a proxy, a database collating relevant soil, organic matter and sediment properties could serve as an initial step to identify which soil types and erosion scenarios are prone to generate a high uncertainty compared to the use of soil texture in erosion models. Furthermore, it could serve to develop standardized analytical procedures for appropriate description of soil and organic matter as sediment.

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

PubMed

Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

2016-01-01

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Visualization of soil particulate organic matter by means of X-ray CT?

NASA Astrophysics Data System (ADS)

Sleutel, Steven; Van Loo, Denis; Maenhout, Peter; Van Hoorebeke, Luc; Cnudde, Veerle; De Neve, Stefaan

2014-05-01

The role of soil structure in organic matter (OM) stabilization has been primarily investigated through physical fractionation studies operative at the scale of aggregates and smaller organo-mineral particles. By narrowing down soil structure to an arrangement of mineral and organic particles, the majority of studies did not explore the spatial organization of the soil pore network, the actual habitat of microorganisms. The pore structure of soil can have a significant impact on soil processes like OM decomposition by excluding OM from micro-organisms in small pores, by regulating the diffusion of substrates and metabolites and by regulating aeration and presence of moisture. Because of its ability to visualize the 3D architecture of soil non-destructively, X-ray Computed Tomography (CT) is becoming a widespread tool for studying soil pore network structure. However, phase determination of pore space, soil OM, soil mineral matter (MM) and water is often limited even with the latest technological and software advances, allowing high resolution and better quality imaging. Contrast agents commonly used in histology enable enhancement of X-ray attenuation of targeted structures or compounds. Here we report on the first systematic investigation of the use of such X-ray contrast agents for soil research. An evaluation procedure as well as a method to apply the agents to soil samples was developed and applied on reference soil samples. The effectiveness and selectivity of the contrast agents was evaluated for soil organic matter (SOM), MM and water. Several products were found to selectively increase the attenuation of water or SOM. The four agents with the best OM-staining capabilities (Phosphomolybdenic acid (PMA), silver nitrate, lead nitrate and lead acetate) were further tested on an OM-MM mixture. Observed differences in reactivity of the staining agents with MM components were apparent, suggesting that contrasting agents may have to be selected for the specific composition of the soil mineral matrix. Furthermore, techniques such as multiple-energy scanning and K-edge imaging, even in the future perhaps in combination with spectral resolving detectors or spectroscopic techniques can could further enhance the potential benefit from this study of X-ray CT staining agents. The high Z elements of the staining agents have unique and characteristic traits that can be detected or quantified with the abovementioned techniques and methods. We conclude that, given resolution limits and inherent presence of partial volume effects staining, X-ray CT-based localization of discrete SOM particles will be limited to a lower limit of 20-50 µm. Still, the improved 3D visualization of OM and soil pore space opens up possibilities for tailored lab experiments with measures of microbial activity, which could generate new insights in carbon cycling at small scales. In addition, we report on a lab incubation experiment in which CO2 respiration from soil cores was monitored (headspace GC analysis) and an X-ray CT approach yielded soil pore size distributions. We incubated a sandy loam soil (with application of ground grass or sawdust) in 18 small aluminium rings (Ø 1 cm, h 1 cm). Bulk density was adjusted to 1.1 or 1.3 Mg m-3 (compaction) and 6 rings were filled at a coarser Coarse Sand:Fine Sand:Silt+Clay ratio. While compaction induced a strong reduction in the cumulative C mineralization for both grass and sawdust substrates, artificial change to a coarser soil texture only reduced net C mineralization from the added sawdust. There thus appears to be a strong interaction effect between soil pore structure and substrate type on substrate decomposition. Correlation coefficients between the C mineralization rates and volumes of 7 pore size classes (from the X-ray CT data) also showed an increasing positive correlation with increasing pore size. Since any particulate organic matter initially present in the soil was removed prior to the experiment (sieving, ashing the >53µm fraction and recombining with the <53µm fraction), the added OM can be localized by means of X-ray CT. Through on-going image analysis the surrounding porosity of the added grass or sawdust particles is being quantified to further study the interaction between the soil pore structure and substrate decomposition.

Modeling forest site productivity using mapped geospatial attributes within a South Carolina Landscape, USA

DOE PAGES

Parresol, B. R.; Scott, D. A.; Zarnoch, S. J.; ...

2017-12-15

Spatially explicit mapping of forest productivity is important to assess many forest management alternatives. We assessed the relationship between mapped variables and site index of forests ranging from southern pine plantations to natural hardwoods on a 74,000-ha landscape in South Carolina, USA. Mapped features used in the analysis were soil association, land use condition in 1951, depth to groundwater, slope and aspect. Basal area, species composition, age and height were the tree variables measured. Linear modelling identified that plot basal area, depth to groundwater, soils association and the interactions between depth to groundwater and forest group, and between land usemore » in 1951 and forest group were related to site index (SI) (R 2 =0.37), but this model had regression attenuation. We then used structural equation modeling to incorporate error-in-measurement corrections for basal area and groundwater to remove bias in the model. We validated this model using 89 independent observations and found the 95% confidence intervals for the slope and intercept of an observed vs. predicted site index error-corrected regression included zero and one, respectively, indicating a good fit. With error in measurement incorporated, only basal area, soil association, and the interaction between forest groups and land use were important predictors (R2 =0.57). Thus, we were able to develop an unbiased model of SI that could be applied to create a spatially explicit map based primarily on soils as modified by past (land use and forest type) and recent forest management (basal area).« less

Modeling forest site productivity using mapped geospatial attributes within a South Carolina Landscape, USA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parresol, B. R.; Scott, D. A.; Zarnoch, S. J.

Spatially explicit mapping of forest productivity is important to assess many forest management alternatives. We assessed the relationship between mapped variables and site index of forests ranging from southern pine plantations to natural hardwoods on a 74,000-ha landscape in South Carolina, USA. Mapped features used in the analysis were soil association, land use condition in 1951, depth to groundwater, slope and aspect. Basal area, species composition, age and height were the tree variables measured. Linear modelling identified that plot basal area, depth to groundwater, soils association and the interactions between depth to groundwater and forest group, and between land usemore » in 1951 and forest group were related to site index (SI) (R 2 =0.37), but this model had regression attenuation. We then used structural equation modeling to incorporate error-in-measurement corrections for basal area and groundwater to remove bias in the model. We validated this model using 89 independent observations and found the 95% confidence intervals for the slope and intercept of an observed vs. predicted site index error-corrected regression included zero and one, respectively, indicating a good fit. With error in measurement incorporated, only basal area, soil association, and the interaction between forest groups and land use were important predictors (R2 =0.57). Thus, we were able to develop an unbiased model of SI that could be applied to create a spatially explicit map based primarily on soils as modified by past (land use and forest type) and recent forest management (basal area).« less

Development of soils and communities of plants and arbuscular mycorrhizal fungi on West Virginia surface mines.

PubMed

Levy, Michael A; Cumming, Jonathan R

2014-11-01

Surface mining followed by reclamation to pasture is a major driver of land use and cover change in Appalachia. Prior research suggests that many aspects of ecosystem recovery are either slow or incomplete. We examined ecosystem structure-including soil physical and chemical properties, arbuscular mycorrhizal fungal (AMF) infectivity and community composition, and plant diversity and community composition-on a chronosequence of pasture-reclaimed surface mines and a non-mined pasture in northern West Virginia. Surface mining and reclamation dramatically altered ecosystem structure. Some aspects of ecosystem structure, including many measures of soil chemistry and infectivity of AMF, returned rapidly to levels found on the non-mined reference site. Other aspects of ecosystem structure, notably soil physical properties and AMF and plant communities, showed incomplete or no recovery over the short-to-medium term. In addition, invasive plants were prevalent on reclaimed mine sites. The results point to the need for investigation on how reclamation practices could minimize establishment of exotic invasive plant species and reduce the long-term impacts of mining on ecosystem structure and function.

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

PubMed Central

Narr, Anja; Nawaz, Ali; Wick, Lukas Y.; Harms, Hauke; Chatzinotas, Antonis

2017-01-01

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors. PMID:29067022

Nanomineralogy as a new dimension in understanding elusive geochemical processes in soils: The case of low-solubility-index elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schindler, Michael; Hochella, Michael F.

2016-05-20

Nanomineralogy is a new dimension in understanding chemical processes in soils. These processes are revealed at the nanoscale within the structures and compositions of phases that heretofore were not even known to exist in the soils in which they are found. The discovery and understanding of soil chemistry in this way is best accessible via a combination of focused ion beam technology (for sample preparation) and high resolution, analytical transmission electron microscopy (for phase identification). We have used this scientific framework and these techniques to decipher past and present chemical processes in a soil in Sudbury, Ontario, Canada that hasmore » been impacted by both smelter contamination (acidification) and subsequent remediation within the past century. In this study, we use these methods to investigate mobilization and sequestration of the relatively immobile elements Al, Ti and Zr. In a micrometer-thick alteration layer on an albite grain, a first generation of clay minerals represents weathering of the underlying mineral prior to the acidification of the soils. Complex assemblages of Ti- and Zr-bearing nanophases occur on the surfaces of Fe-(hydr)oxide crystals and are the result of the dissolution of silicates and oxides and the mobilization of Ti- and Zr-bearing colloids under acidic conditions. These phases include anatase (TiO2), kleberite (Fe3+Ti6O11(OH)5) Ti4O7, baddelyite (ZrO2), a structural analogue to kelyshite (NaZr[Si2O6(OH)]) and authigenic zircon (ZrSiO4). Subsequent remediation of the acidic soils has resulted in the sequestration of Al and in the neoformation of the clay minerals kaolinite, smectite and illite. These complex mineral assemblages form a porous layer that controls the interaction of the underlying mineral with the environment.« less

Probing the rhizosphere to define mineral organic relationships

NASA Astrophysics Data System (ADS)

Schulz, M. S.; Dohnalkova, A.; Stonestrom, D. A.

2016-12-01

Soil organic matter (SOM) accumulation and stabilization over time is an important process as soils are a large carbon reservoir in which feedbacks under changing climates are unclear. The association of SOM with poorly crystalline or short-range-ordered secondary minerals has been shown to be important for carbon stabilization. Commonly used soil extraction techniques display correlations of SOM with secondary phases but do not show causation. The fate of root exudates in soils and processes controlling exudate associations with mineral phases are as yet structurally undefined. Sub-micron exploration of in-situ relations provides valuable information on SOM-mineral interactions. Soils of the Santa Cruz (California) marine terrace chronosequence are used to illustrate changes in deep (> 1 m) rhizosphere through time. Cracks and soil ped faces are sites of high root density and organic matter (biofilm or mucilage) deposition. We employ a variety of scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM) techniques for high resolution imaging and elemental analyses of deep rhizosphere and associated carbon mineral interactions. In these coastal prairie soils microscopy reveals secondary clay minerals associated with and possibly forming from organic-rich mucilage that occurs along the aforementioned rooting networks on fracture surfaces. We hypothesize that the production of secondary clays in the rhizosphere is an important mode of C incorporation into secondary minerals.

Analysing Structure Dynamics in Arable Soils using X-ray Micro-Tomography

NASA Astrophysics Data System (ADS)

Schlüter, S.; Weller, U.; Vogel, H.-J.

2009-04-01

Structure is a dynamic property of soil. It interacts with many biotic and abiotic features and controls various soil functions. We analyzed soil structure within different plots of the ''Static Fertilisation Experiment'' at the agricultural research station in Bad Lauchstaedt (Germany) using X-ray micro tomography. The aim was to investigate in how far different levels of organic carbon, increased microbial activity and enhanced plant growth affects structural properties of an arable soil. Since 106 years one plot has experienced a constant application of farmyard manure and fertilisers, whereas the other has never been fertilised in this period. Intact soil cores from the chernozem soil at the two plots were taken from a depth of 5 to 15 cm (Ap-horizon) and 35 to 45 cm (Ah-horizon) to analyse structural changes with depth and in two different seasons (spring and summer) to investigate structure dynamics. The pore structure was analysed by quantifying the mean geometrical and topological characteristics of the pore network as a function of pore size. This was done by a combination of Minkowski functionals and morphological size distibution. For small structural features close to the image resolution the results clearly depend on the applied filtering technique and segmentation thresholds. Therefore the application of different image enhancement techniques is discussed. Furthermore, a new method for an automated determination of grey value thesholds for the segmentation of CT-images into pore space and solid is developed and evaluated. We highlight the relevance of image resolution for structure analysis. Results of the structure analysis reveal that the spring samples of the ploughed layer (Ap-horizon) from the fertilised plot have significantly higher macroporosities (P < 0.05) than those from the non-fertilised plot. The internal connectivity of the pore network is better in the fertilised plot and the pore size distribution was found to be different, too. The differences in porosity and pore connectivity increase from spring to summer. Both plots were compacted by a rolling machine in late winter. So the difference in structure dynamics is interpreted as an enhanced structure resiliency in the fertilised and carbon enriched plot after that compaction. A comparison with porosity features of a nearby reference profil under grassland demonstrates that the impact of tillage on pore structure is higher than the different contents in organic carbon. The carbon enriched horizon beneath the ploughed layer (Ah-horizon) shows no differences in pore size distribution and connectivity as a function of fertilisation. Thus, at that soil depth, no long-term effects of fertilization in terms of soil structure are detectable. Obviously, the highly different energy input during 106 years only affects the structure of the top soil.

Ecogeomorphology of Spartina patens-dominated tidal marshes: Soil organic matter accumulation, marsh elevation dynamics, and disturbance

USGS Publications Warehouse

Cahoon, D.R.; Ford, M.A.; Hensel, P.F.; Fagherazzi, Sergio; Marani, Marco; Blum, Linda K.

2004-01-01

Marsh soil development and vertical accretion in Spartina patens (Aiton) Muhl.-dominated tidal marshes is largely dependent on soil organic matter accumulation from root-rhizome production and litter deposition. Yet there are few quantitative data sets on belowground production and the relationship between soil organic matter accumulation and soil elevation dynamics for this marsh type. Spartina patens marshes are subject to numerous stressors, including sea-level rise, water level manipulations (i.e., flooding and draining) by impoundments, and prescribed burning. These stressors could influence long-term marsh sustainability by their effect on root production, soil organic matter accumulation, and soil elevation dynamics. In this review, we summarize current knowledge on the interactions among vegetative production, soil organic matter accumulation and marsh elevation dynamics, or the ecogeomorphology, of Spartina patens-dominated tidal marshes. Additional studies are needed of belowground production/decomposition and soil elevation change (measured simultaneously) to better understand the links among soil organic matter accumulation, soil elevation change, and disturbance in this marsh type. From a management perspective, we need to better understand the impacts of disturbance stressors, both lethal and sub-lethal, and the interactive effect of multiple stressors on soil elevation dynamics in order to develop better management practices to safeguard marsh sustainability as sea level rises.

Cemented Volcanic Soils, Martian Spectra and Implications for the Martian Climate

NASA Technical Reports Server (NTRS)

Bishop, J. L.; Schiffman, P.; Drief, A.; Southard, R. J.

2004-01-01

Cemented soils formed via reactions with salts are studied here and provide information about the climate when they formed. Spectroscopic and microprobe studies have been performed on cemented volcanic crusts in order to learn about the composition of these materials, how they formed, and what they can tell us about climatic interactions with surface material on Mars to form cemented soils. These crusts include carbonate, sulfate and opaline components that may all be present in cemented soil units on Mars.

[Identification of the cumulative eco-environment effect of coal-electricity integration based on interpretative structural model].

PubMed

Han, Lin Wei; Fu, Xiao; Yan, Yan; Wang, Chen Xing; Wu, Gang

2017-05-18

In order to determine the cumulative eco-environmental effect of coal-electricity integration, we selected 29 eco-environmental factors including different development and construction activities of coal-electricity integration, soil, water, atmospheric conditions, biology, landscape, and ecology. Literature survey, expert questionnaire and interview were conducted to analyze the interactive relationships between different factors. The structure and correlations between the eco-environmental factors influenced by coal-electricity integration activities were analyzed using interpretive structural modeling (ISM) and the cumulative eco-environment effect of development and construction activities was determined. A research and evaluation framework for the cumulative eco-environmental effect was introduced in addition to specific evaluation and management needs. The results of this study would provide a theoretical and technical basis for planning and management of coal-electricity integration development activities.

Nitrogen-mediated effects of elevated CO2 on intra-aggregate soil pore structure.

PubMed

Caplan, Joshua S; Giménez, Daniel; Subroy, Vandana; Heck, Richard J; Prior, Stephen A; Runion, G Brett; Torbert, H Allen

2017-04-01

Soil pore structure has a strong influence on water retention, and is itself influenced by plant and microbial dynamics such as root proliferation and microbial exudation. Although increased nitrogen (N) availability and elevated atmospheric CO 2 concentrations (eCO 2 ) often have interacting effects on root and microbial dynamics, it is unclear whether these biotic effects can translate into altered soil pore structure and water retention. This study was based on a long-term experiment (7 yr at the time of sampling) in which a C 4 pasture grass (Paspalum notatum) was grown on a sandy loam soil while provided factorial additions of N and CO 2 . Through an analysis of soil aggregate fractal properties supported by 3D microtomographic imagery, we found that N fertilization induced an increase in intra-aggregate porosity and a simultaneous shift toward greater accumulation of pore space in larger aggregates. These effects were enhanced by eCO 2 and yielded an increase in water retention at pressure potentials near the wilting point of plants. However, eCO 2 alone induced changes in the opposite direction, with larger aggregates containing less pore space than under control conditions, and water retention decreasing accordingly. Results on biotic factors further suggested that organic matter gains or losses induced the observed structural changes. Based on our results, we postulate that the pore structure of many mineral soils could undergo N-dependent changes as atmospheric CO 2 concentrations rise, having global-scale implications for water balance, carbon storage, and related rhizosphere functions. © 2016 John Wiley & Sons Ltd.

Nematode Community Response to Green Infrastructure Design in a Semiarid City.

PubMed

Pavao-Zuckerman, Mitchell A; Sookhdeo, Christine

2017-05-01

Urbanization affects ecosystem function and environmental quality through shifts in ecosystem fluxes that are brought on by features of the built environment. Green infrastructure (GI) has been suggested as a best management practice (BMP) to address urban hydrologic and ecological impacts of the built environment, but GI practice has only been studied from a limited set of climatic conditions and disciplinary approaches. Here, we evaluate GI features in a semiarid city from the perspective of soil ecology through the application of soil nematode community analysis. This study was conducted to investigate soil ecological interactions in small-scale GI as a means of assessing curb-cut rain garden basin design in a semiarid city. We looked at the choice of mulching approaches (organic vs. rock) and how this design choice affects the soil ecology of rain basins in Tucson, AZ. We sampled soils during the monsoon rain season and assessed the soil nematode community as a bioindicator of soil quality and biogeochemical processes. We found that the use of organic mulch in GI basins promotes enhanced soil organic matter contents and larger nematode populations. Nematode community indices point to enhanced food web structure in streetscape rain garden basins that are mulched with organic material. Results from this study suggest that soil management practices for GI can help promote ecological interactions and ecosystem services in urban ecosystems. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Interactive initialization of heat flux parameters for numerical models using satellite temperature measurements

NASA Technical Reports Server (NTRS)

Carlson, T. N. (Principal Investigator)

1982-01-01

Progress made in HCMM research, including testing the interactive minicomputer system and preparation of a paper on the analysis of regional scale soil moisture patterns, is summarized. An exhibit on remote sensing including a videotape display of HCMM images, most of them of the State College area, was prepared.

Long-term controls of soil organic carbon with depth and time: a case study from the Cowlitz River Chronosequence, WA USA

USGS Publications Warehouse

Lawrence, Corey R.; Harden, Jennifer W.; Xu, Xiaomei; Schulz, Marjorie S.; Trumbore, Susan E.

2015-01-01

Over timescales of soil development (millennia), the capacity of soils to stabilize soil organic carbon (SOC) is linked to soil development through changes in soil mineralogy and other soil properties. In this study, an extensive dataset of soil profile chemistry and mineralogy is compiled from the Cowlitz River Chronosequence (CRC), WA USA. The CRC soils range in age from 0.25 to 1200 kyr, spanning a developmental gradient encompassing clear changes in soil mineralogy, chemistry, and surface area. Comparison of these and other metrics of soil development with SOC properties reveal several relationships that may be diagnostic of the long-term coupling of soil development and C cycling. Specifically, SOC content was significantly correlated with sodium pyrophosphate extractable metals emphasizing the relevance of organo-metal complexes in volcanic soils. The depth distributions of organo-metals and other secondary weathering products, including the kaolin and short-range order (SRO) minerals, support the so-called “binary composition” of volcanic soils. The formation of organo-metal complexes limits the accumulation of secondary minerals in shallow soils, whereas in deep soils with lower SOC content, secondary minerals accumulate. In the CRC soils, secondary minerals formed in deep soils (below 50 cm) including smectite, allophane, Fe-oxides and dominated by the kaolin mineral halloysite. The abundance of halloysite was significantly correlated with bulk soil surface area and 14C content (a proxy for the mean age of SOC), implying enhanced stability of C in deep soils. Allophane, an SRO mineral commonly associated with SOC storage, was not correlated with SOC content or 14C values in CRC soils. We propose conceptual framework to describe these observations based on a general understanding of pedogenesis in volcanic soils, where SOC cycling is coupled with soil development through the formation of and fate of organo-metal or other mobile weathering products. This framework highlights interactions between SOC and soil development, which may be applicable to other soils where organic inputs interact with the products of chemical weathering.

[Stabilization of Cadmium Contaminated Soils by Ferric Ion Modified Attapulgite (Fe/ATP)--Characterizations and Stabilization Mechanism].

PubMed

Rong, Yang; Li, Rong-bo; Zhou, Yong-li; Chen, Jing; Wang, Lin-ling; Lu, Xiao-hua

2015-08-01

Ferric ion modified attapulgite (Fe/ATP) was prepared by impregnation and its structure and morphology were characterized. The toxicity characteristic leaching procedure (TCLP) was used to evaluate the effect of Cadmium( Cd) stabilization in soil with the addition of attapulgite (ATP) and Fe/ATP. The stabilization mechanism of Cd was further elucidated by comparing the morphologies and structure of ATP and Fe/ATP before and after Cd adsorption. Fe/ATP exhibited much better adsorption capacity than ATP, suggesting different adsorption mechanisms occurred between ATP and Fe/ATP. The leaching concentrations of Cd in soil decreased by 45% and 91% respectively, with the addition of wt. 20% ATP and Fe/ATP. The former was attributed to the interaction between Cd2 and --OH groups by chemical binding to form inner-sphere complexes in ATP and the attachment between Cd2+ and the defect sites in ATP framework. Whereas Cd stabilization with Fe/ATP was resulted from the fact that the active centers (--OH bonds or O- sites) on ATP could react with Fe3+ giving Fe--O--Cd-- bridges, which helped stabilize Cd in surface soil. What'more, the ferric oxides and metal hydroxides on the surface of ATP could interact with Cd, probably by the formation of cadmium ferrite. In conclusion, Fe/ATP, which can be easily prepared, holds promise as a potential low-cost and environmental friendly stabilizing agent for remediation of soil contaminated with heavy metals.

Performance of buried pipe installation : technical summary.

DOT National Transportation Integrated Search

2010-05-01

The goal of this research project was to determine the effects of geometric and mechanical parameters characterizing the soil-structure interaction developed in a buried pipe installation. Parameters such as pipe ring stiff ness, bedding thickness, t...

Field study of an integral backwall bridge : final report.

DOT National Transportation Integrated Search

1996-01-01

Integral bridges offer reduced maintenance expenditures, primarily due to the elimination of deck expansion joints. The design of an integral bridge, however, is complicated by the soil-structure interaction associated with thermal movements. It has ...

Carbonyl sulfide exchange in soils for better estimates of ecosystem carbon uptake

DOE PAGES

Whelan, Mary E.; Hilton, Timothy W.; Berry, Joseph A.; ...

2016-03-21

Carbonyl sulfide (COS) measurements are one of the emerging tools to better quantify gross primary production (GPP), the largest flux in the global carbon cycle. COS is a gas with a similar structure to CO 2; COS uptake is thought to be a proxy for GPP. However, soils are a potential source or sink of COS. This study presents a framework for understanding soil–COS interactions. Excluding wetlands, most of the few observations of isolated soils that have been made show small uptake of atmospheric COS. Recently, a series of studies at an agricultural site in the central United States foundmore » soil COS production under hot conditions an order of magnitude greater than fluxes at other sites. To investigate the extent of this phenomenon, soils were collected from five new sites and incubated in a variety of soil moisture and temperature states. We found that soils from a desert, an oak savannah, a deciduous forest, and a rainforest exhibited small COS fluxes, behavior resembling previous studies. However, soil from an agricultural site in Illinois, >800 km away from the initial central US study site, demonstrated comparably large soil fluxes under similar conditions. These new data suggest that, for the most part, soil COS interaction is negligible compared to plant uptake of COS. We present a model that anticipates the large agricultural soil fluxes so that they may be taken into account. Furthermore, while COS air-monitoring data are consistent with the dominance of plant uptake, improved interpretation of these data should incorporate the soil flux parameterizations suggested here.« less

Differences in the Activities of Eight Enzymes from Ten Soil Fungi and Their Possible Influences on the Surface Structure, Functional Groups, and Element Composition of Soil Colloids

PubMed Central

Wang, Wenjie; Li, Yanhong; Wang, Huimei; Zu, Yuangang

2014-01-01

How soil fungi function in soil carbon and nutrient cycling is not well understood by using fungal enzymatic differences and their interactions with soil colloids. Eight extracellular enzymes, EEAs (chitinase, carboxymethyl cellulase, β-glucosidase, protease, acid phosphatase, polyphenol oxidase, laccase, and guaiacol oxidase) secreted by ten fungi were compared, and then the fungi that showed low and high enzymatic activity were co-cultured with soil colloids for the purpose of finding fungi-soil interactions. Some fungi (Gomphidius rutilus, Russula integra, Pholiota adiposa, and Geastrum mammosum) secreted 3–4 enzymes with weak activities, while others (Cyathus striatus, Suillus granulate, Phallus impudicus, Collybia dryophila, Agaricus sylvicola, and Lactarius deliciosus) could secret over 5 enzymes with high activities. The differences in these fungi contributed to the alterations of functional groups (stretching bands of O-H, N-H, C-H, C = O, COO- decreased by 11–60%, while P = O, C-O stretching, O-H bending and Si-O-Si stretching increased 9–22%), surface appearance (disappearance of adhesive organic materials), and elemental compositions (11–49% decreases in C1s) in soil colloids. Moreover, more evident changes were generally in high enzymatic fungi (C. striatus) compared with low enzymatic fungi (G. rutilus). Our findings indicate that inter-fungi differences in EEA types and activities might be responsible for physical and chemical changes in soil colloids (the most active component of soil matrix), highlighting the important roles of soil fungi in soil nutrient cycling and functional maintenance. PMID:25398013

Differences in the activities of eight enzymes from ten soil fungi and their possible influences on the surface structure, functional groups, and element composition of soil colloids.

PubMed

Wang, Wenjie; Li, Yanhong; Wang, Huimei; Zu, Yuangang

2014-01-01

How soil fungi function in soil carbon and nutrient cycling is not well understood by using fungal enzymatic differences and their interactions with soil colloids. Eight extracellular enzymes, EEAs (chitinase, carboxymethyl cellulase, β-glucosidase, protease, acid phosphatase, polyphenol oxidase, laccase, and guaiacol oxidase) secreted by ten fungi were compared, and then the fungi that showed low and high enzymatic activity were co-cultured with soil colloids for the purpose of finding fungi-soil interactions. Some fungi (Gomphidius rutilus, Russula integra, Pholiota adiposa, and Geastrum mammosum) secreted 3-4 enzymes with weak activities, while others (Cyathus striatus, Suillus granulate, Phallus impudicus, Collybia dryophila, Agaricus sylvicola, and Lactarius deliciosus) could secret over 5 enzymes with high activities. The differences in these fungi contributed to the alterations of functional groups (stretching bands of O-H, N-H, C-H, C = O, COO- decreased by 11-60%, while P = O, C-O stretching, O-H bending and Si-O-Si stretching increased 9-22%), surface appearance (disappearance of adhesive organic materials), and elemental compositions (11-49% decreases in C1s) in soil colloids. Moreover, more evident changes were generally in high enzymatic fungi (C. striatus) compared with low enzymatic fungi (G. rutilus). Our findings indicate that inter-fungi differences in EEA types and activities might be responsible for physical and chemical changes in soil colloids (the most active component of soil matrix), highlighting the important roles of soil fungi in soil nutrient cycling and functional maintenance.

Plant-soil-microbe interactions regulating soil C storage

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.

2016-12-01

Integration across disciplines is required to identify the emergent microbial scale properties that regulate the release or occlusion of plant inputs in soil organic matter. To investigate how micro-scale processes influence soil carbon cycling, we measured microbial community composition and activity within soil aggregates monthly over two growing seasons of a long-term bioenergy field experiment. Using a biologically sensitive sieving technique, soil aggregates were isolated and microbial community activity and composition were measured. This aggregate approach revealed biogeochemical processes regulating C cycling that are not detected using whole soil approaches. Soil aggregation influenced microbe-substrate interactions, where diversified perennial grassland systems supported greater aggregation and reduced severity of aggregate turnover compared to corn systems. Aggregate turnover and concurrent increases in activity resulted in greater microbial biomass and physical protection of soil organic matter in prairie systems, especially fertilized prairies. Fertilized prairie enhanced microbial biomass, enzyme activity, and soil aggregation despite greater root biomass in unfertilized prairie. Independent of ecosystem or sampling date, N-acetyl-glucosaminidase activity and Nitrospirae abundance was greatest in large macroaggregates (>2000 µm), which harbored the highest C:N; cellobiohydrolase activity and Acidobacteria abundance was greatest in microaggregates (<250 µm) which had the lowest C:N. Aggregate fractions differed in microbial community composition (bacteria, archaea, and fungi) and potential enzyme activity, independent of cropping system. Microaggregates harbored significantly greater microbial diversity and richness across all bioenergy cropping systems. Together these results suggest that by mediating access to substrates, soil structure (aggregates) can influence the microbial community composition and extracellular enzyme activity to regulate ecosystem scale decomposition of soil organic matter.

Pore-Scale Effects of Soil Structure And Microbial EPS Production On Soil Water Retention

NASA Astrophysics Data System (ADS)

Orner, E.; Anderson, E.; Rubinstein, R. L.; Chau, J. F.; Shor, L. M.; Gage, D. J.

2013-12-01

Climate-induced changes to the hydrological cycle will increase the frequency of extreme weather events including powerful storms and prolonged droughts. Moving forward, one of the major factors limiting primary productivity in terrestrial ecosystems will be sub-optimal soil moisture. We focus here on the ability of soils to retain moisture under drying conditions. A soil's ability to retain moisture is influenced by many factors including its texture, its structure, and the activities of soil microbes. In soil microcosms, the addition of small amounts of microbially-produced extracellular polymeric substances (EPS) can dramatically shift moisture retention curves. The objective of this research is to better understand how soil structure and EPS may act together to retain moisture in unsaturated soils. Replicate micromodels with exactly-conserved 2-D physical geometry were initially filled with aqueous suspensions of one of two types of bacteria: one mutant was ultra- muccoid and the other was non-muccoid. Replicate micromodels were held at a fixed, external, relative humidity, and the position of the air-water interface was imaged over time as water evaporates. There was no forced convection of air or water inside the micromodels: drying was achieved by water evaporation and diffusion alone. We used a fully automated, inverted microscope to image replicate drying lanes each with dimensions of 1 mm x 10 mm. A complete set of images was collected every 30 minutes for 30 hours. The results show devices loaded with the highly muccoid strain remained >40% hydrated for 13 h, while devices loaded with the non-muccoid remained >40% hydrated for only 6 h, and were completely dry by 13 h. Current work is comparing interfacial water fluxes in structured and unstructured settings, and is attempting to model the synergistic effects of soil structure and EPS content on moisture retention in real soils. This research may allow more accurate description of naturally-occurring feedbacks between the soil carbon and water cycles, and may enable agriculture biotechnology that enhances natural soil processes for improved resiliency of terrestrial ecosystems.

Future soil moisture and temperature extremes imply expanding suitability for rainfed agriculture in temperate drylands

USGS Publications Warehouse

Bradford, John B.; Schlaepfer, Daniel R.; Lauenroth, William K.; Yackulic, Charles B.; Duniway, Michael C.; Hall, Sonia A.; Jia, Gensuo; Jamiyansharav, Khishigbayar; Munson, Seth M.; Wilson, Scott D.; Tietjen, Britta

2017-01-01

The distribution of rainfed agriculture is expected to respond to climate change and human population growth. However, conditions that support rainfed agriculture are driven by interactions among climate, including climate extremes, and soil moisture availability that have not been well defined. In the temperate regions that support much of the world’s agriculture, these interactions are complicated by seasonal temperature fluctuations that can decouple climate and soil moisture. Here, we show that suitability to support rainfed agriculture can be effectively represented by the interactive effects of just two variables: suitability increases where warm conditions occur with wet soil, and suitability decreases with extreme high temperatures. 21st century projections based on ecohydrological modeling of downscaled climate forecasts imply geographic shifts and overall increases in the area suitable for rainfed agriculture in temperate regions, especially at high latitudes, and pronounced, albeit less widespread, declines in suitable areas in low latitude drylands, especially in Europe. These results quantify the integrative direct and indirect impact of rising temperatures on rainfed agriculture.

Development of p-y curves of laterally loaded piles in cohesionless soil.

PubMed

Khari, Mahdy; Kassim, Khairul Anuar; Adnan, Azlan

2014-01-01

The research on damages of structures that are supported by deep foundations has been quite intensive in the past decade. Kinematic interaction in soil-pile interaction is evaluated based on the p-y curve approach. Existing p-y curves have considered the effects of relative density on soil-pile interaction in sandy soil. The roughness influence of the surface wall pile on p-y curves has not been emphasized sufficiently. The presented study was performed to develop a series of p-y curves for single piles through comprehensive experimental investigations. Modification factors were studied, namely, the effects of relative density and roughness of the wall surface of pile. The model tests were subjected to lateral load in Johor Bahru sand. The new p-y curves were evaluated based on the experimental data and were compared to the existing p-y curves. The soil-pile reaction for various relative density (from 30% to 75%) was increased in the range of 40-95% for a smooth pile at a small displacement and 90% at a large displacement. For rough pile, the ratio of dense to loose relative density soil-pile reaction was from 2.0 to 3.0 at a small to large displacement. Direct comparison of the developed p-y curve shows significant differences in the magnitude and shapes with the existing load-transfer curves. Good comparison with the experimental and design studies demonstrates the multidisciplinary applications of the present method.

Development of p-y Curves of Laterally Loaded Piles in Cohesionless Soil

PubMed Central

Khari, Mahdy; Kassim, Khairul Anuar; Adnan, Azlan

2014-01-01

The research on damages of structures that are supported by deep foundations has been quite intensive in the past decade. Kinematic interaction in soil-pile interaction is evaluated based on the p-y curve approach. Existing p-y curves have considered the effects of relative density on soil-pile interaction in sandy soil. The roughness influence of the surface wall pile on p-y curves has not been emphasized sufficiently. The presented study was performed to develop a series of p-y curves for single piles through comprehensive experimental investigations. Modification factors were studied, namely, the effects of relative density and roughness of the wall surface of pile. The model tests were subjected to lateral load in Johor Bahru sand. The new p-y curves were evaluated based on the experimental data and were compared to the existing p-y curves. The soil-pile reaction for various relative density (from 30% to 75%) was increased in the range of 40–95% for a smooth pile at a small displacement and 90% at a large displacement. For rough pile, the ratio of dense to loose relative density soil-pile reaction was from 2.0 to 3.0 at a small to large displacement. Direct comparison of the developed p-y curve shows significant differences in the magnitude and shapes with the existing load-transfer curves. Good comparison with the experimental and design studies demonstrates the multidisciplinary applications of the present method. PMID:24574932

Method and apparatus to image biological interactions in plants

DOEpatents

Weisenberger, Andrew; Bonito, Gregory M.; Reid, Chantal D.; Smith, Mark Frederick

2015-12-22

A method to dynamically image the actual translocation of molecular compounds of interest in a plant root, root system, and rhizosphere without disturbing the root or the soil. The technique makes use of radioactive isotopes as tracers to label molecules of interest and to image their distribution in the plant and/or soil. The method allows for the study and imaging of various biological and biochemical interactions in the rhizosphere of a plant, including, but not limited to, mycorrhizal associations in such regions.

Three phase heat and mass transfer model for unsaturated soil freezing process: Part 1 - model development

NASA Astrophysics Data System (ADS)

Xu, Fei; Zhang, Yaning; Jin, Guangri; Li, Bingxi; Kim, Yong-Song; Xie, Gongnan; Fu, Zhongbin

2018-04-01

A three-phase model capable of predicting the heat transfer and moisture migration for soil freezing process was developed based on the Shen-Chen model and the mechanisms of heat and mass transfer in unsaturated soil freezing. The pre-melted film was taken into consideration, and the relationship between film thickness and soil temperature was used to calculate the liquid water fraction in both frozen zone and freezing fringe. The force that causes the moisture migration was calculated by the sum of several interactive forces and the suction in the pre-melted film was regarded as an interactive force between ice and water. Two kinds of resistance were regarded as a kind of body force related to the water films between the ice grains and soil grains, and a block force instead of gravity was introduced to keep balance with gravity before soil freezing. Lattice Boltzmann method was used in the simulation, and the input variables for the simulation included the size of computational domain, obstacle fraction, liquid water fraction, air fraction and soil porosity. The model is capable of predicting the water content distribution along soil depth and variations in water content and temperature during soil freezing process.

Chemical and Physical Interactions of Martian Surface Material

NASA Astrophysics Data System (ADS)

Bishop, J. L.

1999-09-01

A model of alteration and maturation of the Martian surface material is described involving both chemical and physical interactions. Physical processes involve distribution and mixing of the fine-grained soil particles across the surface and into the atmosphere. Chemical processes include reaction of sulfate, salt and oxidizing components of the soil particles; these agents in the soils deposited on rocks will chew through the rock minerals forming coatings and will bind surface soils together to form duricrust deposits. Formation of crystalline iron oxide/oxyhydroxide minerals through hydrothermal processes and of poorly crystalline and amorphous phases through palagonitic processes both contribute to formation of the soil particles. Chemical and physical alteration of these soil minerals and phases contribute to producing the chemical, magnetic and spectroscopic character of the Martian soil as observed by Mars Pathfinder and Mars Global Surveyor. Minerals such as maghemite/magnetite and jarosite/alunite have been observed in terrestrial volcanic soils near steam vents and may be important components of the Martian surface material. The spectroscopic properties of several terrestrial volcanic soils containing these minerals have been analyzed and evaluated in terms of the spectroscopic character of the surface material on Mars.

76 FR 35511 - Decommissioning Planning

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-17

..., which includes the site's subsurface soil and groundwater. Licensees also may be required to perform... structures, materials, soils, groundwater, and other media at a site resulting from activities under the.... Certain operational events (e.g., slow, long-term leaks), particularly those that cause subsurface soil...

Spectral Survey of Irrigated Region Corps and Soils

NASA Technical Reports Server (NTRS)

1971-01-01

The applications of remote sensing techniques to spectral surveys of irrigation, crops, and soils are reported. Topics discussed include: (1) canopy temperature as an indication of plant water stress, (2) temperature of soils and of crop canopies differing in water conditions, (3) ERTS project, (4) spectrum matching and pattern recognition, (5) photographic procedures and interpretation, (6) interaction of light with plants, and (7) plant physiological and histological factors.

23 CFR 650.205 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

..., STRUCTURES, AND HYDRAULICS Erosion and Sediment Control on Highway Construction Projects § 650.205... transporting of soil particles by water or wind, including actions that limit the area of exposed soil and... completion of the project. Pollutants are substances, including sediment, which cause deterioration of water...

23 CFR 650.205 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., STRUCTURES, AND HYDRAULICS Erosion and Sediment Control on Highway Construction Projects § 650.205... transporting of soil particles by water or wind, including actions that limit the area of exposed soil and... completion of the project. Pollutants are substances, including sediment, which cause deterioration of water...

23 CFR 650.205 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., STRUCTURES, AND HYDRAULICS Erosion and Sediment Control on Highway Construction Projects § 650.205... transporting of soil particles by water or wind, including actions that limit the area of exposed soil and... completion of the project. Pollutants are substances, including sediment, which cause deterioration of water...

23 CFR 650.205 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., STRUCTURES, AND HYDRAULICS Erosion and Sediment Control on Highway Construction Projects § 650.205... transporting of soil particles by water or wind, including actions that limit the area of exposed soil and... completion of the project. Pollutants are substances, including sediment, which cause deterioration of water...

23 CFR 650.205 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., STRUCTURES, AND HYDRAULICS Erosion and Sediment Control on Highway Construction Projects § 650.205... transporting of soil particles by water or wind, including actions that limit the area of exposed soil and... completion of the project. Pollutants are substances, including sediment, which cause deterioration of water...

Phoresy of the entomopathogenic nematode Steinernema feltiae by the earthworm Eisenia fetida.

PubMed

Campos-Herrera, Raquel; Trigo, Dolores; Gutiérrez, Carmen

2006-05-01

The free-living stage of entomopathogenic nematodes occurs in soil, and is an environmental-friendly alternative for biological control. However, their dispersal capability is limited. Earthworms improve soil characteristics, changing soil structure and influencing many edaphic organisms. Thus, earthworms could be used as vectors to introduce/disperse beneficial organisms. Nevertheless this interaction has not been studied in detail. This study presents the infectivity results of Steinernema feltiae after passing through the Eisenia fetida gut. Although entomopathogenic nematodes have no deleterious effects on earthworms, their passage through E. fetida gut seriously affected their mobility and virulence.

Digging the termite way: crowding simple robots to excavate ramification structures

NASA Astrophysics Data System (ADS)

Bardunias, Paul

The complex ramification network that termites excavate in soil in search of resources has been shown to emerge from interactions between individuals during periodic crowding at the tips of tunnels. Excavation in these social insects is carried out by a rotation of termites removing soil from the tip of an expanding tunnel and depositing it back along the tunnel walls. Bristle bots, modified to either rock or turn on contact with soil in an artificial tunnel, were used to replicate this process. As in termites, congestion at tunnel tips leads to the widening and branching of tunnels.

CENTRIFUGAL VIBRATION TEST OF RC PILE FOUNDATION

NASA Astrophysics Data System (ADS)

Higuchi, Shunichi; Tsutsumiuchi, Takahiro; Otsuka, Rinna; Ito, Koji; Ejiri, Joji

It is necessary that nonlinear responses of structures are clarified by soil-structure interaction analysis for the purpose of evaluating the seismic performances of underground structure or foundation structure. In this research, centrifuge shake table tests of reinforced concrete pile foundation installed in the liquefied ground were conducted. Then, finite element analyses for the tests were conducted to confirm an applicability of the analytical method by comparing the experimental results and analytical results.

Laboratory incubation experiments assessing the factor interactions affecting urine-derived nitrous oxide emissions from spatially and temporally variable upland pastures

NASA Astrophysics Data System (ADS)

Charteris, Alice; Loick, Nadine; Marsden, Karina; Chadwick, Dave; Whelan, Mick; Rao Ravella, Sreenivas; Mead, Andrew; Cardenas, Laura

2017-04-01

Urine patches deposited to soils by grazing animals represent hot-spots of nitrous oxide (N2O) emissions (Hargreaves et al., 2015), a powerful greenhouse gas (GHG) and precursor of ozone depletion in the stratosphere. Urine N2O emissions are produced via nitrification of ureolysis-derived ammonium (NH4+) and/or subsequent nitrite (NO2-) and nitrate (NO3-) denitrification (Kool et al., 2006). The dominant process and the N2O fluxes generated depend on interactions between urine characteristics (e.g. nitrogen [N] concentration and volume), soil characteristics (e.g. carbon [C] availability and pH) and preceding and prevailing environmental conditions (e.g. soil moisture and temperature; Bergstermann et al., 2011; Butterbach-Bahl et al., 2013; Dijkstra et al., 2013). The spatial and temporal variability of these interactions in grazing systems is potentially large and greatly increases the uncertainty associated with N2O emission estimates from such systems. In particular, the contribution of extensively managed upland agroecosystems, which occupy ca. 5.5 million hectares in the UK and provide the bulk of land for sheep farming (Pollott & Stone, 2004), to UK GHG emissions is poorly defined. Improving understanding of the interactions between the wide range of factors affecting urine-derived N2O production and emission from pasture soils and considering this in the context of the spatial and temporal variability of the grazing environment could therefore be extremely valuable in improving the accuracy of N2O emission estimates from such systems. The factorial laboratory incubation experiments presented have been designed to assess the interactive effects of factors such as urine N concentration, volume and soil moisture affecting soil N2O (and nitric oxide [NO], nitrogen gas [N2] and carbon dioxide [CO2]) production and emissions (García-Marco et al., 2014) using the state-of-the-art Denitrification Incubation System (DENIS). This work forms part of a wider project aimed at improving understanding of the spatial and temporal interactions between sheep grazing behaviour, forage selection, urine composition and edaphic factors to increase the accuracy of direct N2O emission estimates from extensive upland systems. Two upland pastures at Henfaes Research Centre (Bangor University) are being used for field measurements and the laboratory incubation experiments have been designed to reflect these systems. This includes using soils sampled by non-hierarchical clustering to accurately represent the sites, re-packed in layers (to field-measured bulk density) and selecting factors and levels based on data from field experiments. The relationships between N2O fluxes and the N2O:N2 mole fraction resulting from factor interactions will be used in a pasture-scale model of upland N2O emissions which integrates the spatial and temporal variability of sheep diet and behaviour, urine deposition characteristics, topography and soil physico-chemical measurements. The approach will generate more accurate N2O emission estimates from extensive grazing systems. The improved process-level understanding gained will aid the development of appropriate mitigation strategies. Bergstermann (2011) SBB 43, 240-250. Butterbach-Bahl (2013) Phil. T. R. Soc. B 368, DOI:10.1098/rstb.2013.0122. Dijkstra (2013) Animal 7, 292-302. García-Marco (2014) EJSS 65, 573-583. Hargreaves (2015) Environ. & Nat. Res. Res. 5, DOI:10.5539/enrr.v5n4p1. Kool (2006) SBB 38, 1757-1763. Pollott & Stone (2004) The Breeding Structure of the British Sheep Industry 2003, Defra, UK.

Interactions between soil thermal and hydrological dynamics in the response of Alaska ecosystems to fire disturbance

Treesearch

Shuhua Yi; David McGuire; Jennifer Harden; Eric Kasischke; Kristen Manies; Larr Hinzman; Anna Liljedahl; Jim Randerson; Heping Liu; Vladimire Romanovsky; Sergei Marchenko; Yongwon Kim

2009-01-01

Soil temperature and moisture are important factors that control many ecosystem processes. However, interactions between soil thermal and hydrological processes are not adequately understood in cold regions, where the frozen soil, fire disturbance, and soil drainage play important roles in controlling interactions among these processes. These interactions were...

Crabs Mediate Interactions between Native and Invasive Salt Marsh Plants: A Mesocosm Study

PubMed Central

Zhang, Xiao-dong; Jia, Xin; Chen, Yang-yun; Shao, Jun-jiong; Wu, Xin-ru; Shang, Lei; Li, Bo

2013-01-01

Soil disturbance has been widely recognized as an important factor influencing the structure and dynamics of plant communities. Although soil reworkers were shown to increase habitat complexity and raise the risk of plant invasion, their role in regulating the interactions between native and invasive species remains unclear. We proposed that crab activities, via improving soil nitrogen availability, may indirectly affect the interactions between invasive Spartina alterniflora and native Phragmites australis and Scirpus mariqueter in salt marsh ecosystems. We conducted a two-year mesocosm experiment consisting of five species combinations, i.e., monocultures of three species and pair-wise mixtures of invasive and native species, with crabs being either present or absent for each combination. We found that crabs could mitigate soil nitrogen depletion in the mesocosm over the two years. Plant performance of all species, at both the ramet-level (height and biomass per ramet) and plot-level (density, total above- and belowground biomass), were promoted by crab activities. These plants responded to crab disturbance primarily by clonal propagation, as plot-level performance was more sensitive to crabs than ramet-level. Moreover, crab activities altered the competition between Spartina and native plants in favor of the former, since Spartina was more promoted than native plants by crab activities. Our results suggested that crab activities may increase the competition ability of Spartina over native Phragmites and Scirpus through alleviating soil nitrogen limitation. PMID:24023926

Moss Mediates the Influence of Shrub Species on Soil Properties and Processes in Alpine Tundra.

PubMed

Bueno, C Guillermo; Williamson, Scott N; Barrio, Isabel C; Helgadóttir, Ágústa; HiK, David S

2016-01-01

In tundra ecosystems, bryophytes influence soil processes directly and indirectly through interactions with overstory shrub species. We experimentally manipulated moss cover and measured seasonal soil properties and processes under two species of deciduous shrubs with contrasting canopy structures, Salix planifolia pulchra and Betula glandulosa-nana complex. Soil properties (seasonal temperature, moisture and C:N ratios) and processes (seasonal litter decomposition and soil respiration) were measured over twelve months. Shrub species identity had the largest influence on summer soil temperatures and soil respiration rates, which were higher under Salix canopies. Mosses were associated with lower soil moisture irrespective of shrub identity, but modulated the effects of shrubs on winter soil temperatures and soil C:N ratios so that moss cover reduced differences in soil winter temperatures between shrub species and reduced C:N ratios under Betula but not under Salix canopies. Our results suggest a central role of mosses in mediating soil properties and processes, with their influence depending on shrub species identity. Such species-dependent effects need to be accounted for when forecasting vegetation dynamics under ongoing environmental changes.

Moss Mediates the Influence of Shrub Species on Soil Properties and Processes in Alpine Tundra

PubMed Central

Williamson, Scott N.; Barrio, Isabel C.; Helgadóttir, Ágústa; HiK, David S.

2016-01-01

In tundra ecosystems, bryophytes influence soil processes directly and indirectly through interactions with overstory shrub species. We experimentally manipulated moss cover and measured seasonal soil properties and processes under two species of deciduous shrubs with contrasting canopy structures, Salix planifolia pulchra and Betula glandulosa-nana complex. Soil properties (seasonal temperature, moisture and C:N ratios) and processes (seasonal litter decomposition and soil respiration) were measured over twelve months. Shrub species identity had the largest influence on summer soil temperatures and soil respiration rates, which were higher under Salix canopies. Mosses were associated with lower soil moisture irrespective of shrub identity, but modulated the effects of shrubs on winter soil temperatures and soil C:N ratios so that moss cover reduced differences in soil winter temperatures between shrub species and reduced C:N ratios under Betula but not under Salix canopies. Our results suggest a central role of mosses in mediating soil properties and processes, with their influence depending on shrub species identity. Such species-dependent effects need to be accounted for when forecasting vegetation dynamics under ongoing environmental changes. PMID:27760156

When and where does preferential flow matter - from observation to large scale modelling

NASA Astrophysics Data System (ADS)

Weiler, Markus; Leistert, Hannes; Steinbrich, Andreas

2017-04-01

Preferential flow can be of relevance in a wide range of soils and the interaction of different processes and factors are still difficult to assess. As most studies (including our own studies) focusing on the effect of preferential flow are based on relatively high precipitation rates, there is always the question how relevant preferential flow is under natural conditions, considering the site specific precipitation characteristics, the effect of the drying and wetting cycle on the initial soil water condition and shrinkage cracks, the site specific soil properties, soil structure and rock fragments, and the effect of plant roots and soil fauna (e.g. earthworm channels). In order to assess this question, we developed the distributed, process-based model RoGeR (Runoff Generation Research) to include a large number relevant features and processes of preferential flow in soils. The model was developed from a large number of process based research and experiments and includes preferential flow in roots, earthworm channels, along rock fragments and shrinkage cracks. We parameterized the uncalibrated model at a high spatial resolution of 5x5m for the whole state of Baden-Württemberg in Germany using LiDAR data, degree of sealing, landuse, soil properties and geology. As the model is an event based model, we derived typical event based precipitation characteristics based on rainfall duration, mean intensity and amount. Using the site-specific variability of initial soil moisture derived from a water balance model based on the same dataset, we simulated the infiltration and recharge amounts of all event classes derived from the event precipitation characteristics and initial soil moisture conditions. The analysis of the simulation results allowed us to extracts the relevance of preferential flow for infiltration and recharge considering all factors above. We could clearly see a strong effect of the soil properties and land-use, but also, particular for clay rich soils a strong effect of the initial conditions due to the development of soil cracks. Not too surprisingly, the relevance of preferential flow was much lower when considering the whole range of precipitation events as only considering events with a high rainfall intensity. Also, the influence on infiltration and recharge were different. Despite the model can still be improved in particular considering more realistic information about the spatial and temporal variability of preferential flow by soil fauna and plants, the model already shows under what situation we need to be very careful when predicting infiltration and recharge with models considering only longer time steps (daily) or only matrix flow.

Effects of Spatial Variability of Soil Properties on the Triggering of Rainfall-Induced Shallow Landslides

NASA Astrophysics Data System (ADS)

Fan, Linfeng; Lehmann, Peter; Or, Dani

2015-04-01

Naturally-occurring spatial variations in soil properties (e.g., soil depth, moisture, and texture) affect key hydrological processes and potentially the mechanical response of soil to hydromechanical loading (relative to the commonly-assumed uniform soil mantle). We quantified the effects of soil spatial variability on the triggering of rainfall-induced shallow landslides at the hillslope- and catchment-scales, using a physically-based landslide triggering model that considers interacting soil columns with mechanical strength thresholds (represented by the Fiber Bundle Model). The spatial variations in soil properties are represented as Gaussian random distributions and the level of variation is characterized by the coefficient of variation and correlation lengths of soil properties (i.e., soil depth, soil texture and initial water content in this study). The impacts of these spatial variations on landslide triggering characteristics were measured by comparing the times to triggering and landslide volumes for heterogeneous soil properties and homogeneous cases. Results at hillslope scale indicate that for spatial variations of an individual property (without cross correlation), the increasing of coefficient of variation introduces weak spots where mechanical damage is accelerated and leads to earlier onset of landslide triggering and smaller volumes. Increasing spatial correlation length of soil texture and initial water content also induces early landslide triggering and small released volumes due to the transition of failure mode from brittle to ductile failure. In contrast, increasing spatial correlation length of soil depth "reduces" local steepness and postpones landslide triggering. Cross-correlated soil properties generally promote landslide initiation, but depending on the internal structure of spatial distribution of each soil property, landslide triggering may be reduced. The effects of cross-correlation between initial water content and soil texture were investigated in detail at the catchment scale by incorporating correlations of both variables with topography. Results indicate that the internal structure of the spatial distribution of each soil property together with their interplays determine the overall performance of the coupled spatial variability. This study emphasizes the importance of both the randomness and spatial structure of soil properties on landslide triggering and characteristics.

Experimental and analytical investigations of the piles and abutments of integral bridges.

DOT National Transportation Integrated Search

2002-01-01

This research investigated, through experimental and analytical studies, the complex interactions that take place between the structural components of an integral bridge and the adjoining soil. The ability of piles and abutments to withstand thermall...

Land Application of Wastes: An Educational Program. Soil as a Treatment Medium - Module 3, Objectives, Script and Booklet.

ERIC Educational Resources Information Center

Clarkson, W. W.; And Others

This module examines the basic properties of soil which have an influence on the success of land treatment of wastes. These relevant properties include soil texture, soil structure, permeability, infiltration, available water capacity, and cation exchange capacity. Biological, chemical and physical mechanisms work to remove and renovate wastes…

Influence of Precipitation Regime on Microbial Decomposition Patterns in Semi-Arid Ecosystems

NASA Astrophysics Data System (ADS)

Feris, K. P.; Jilek, C.; Huber, D. P.; Reinhardt, K.; deGraaff, M.; Lohse, K.; Germino, M.

2011-12-01

In water-limited semi-arid sagebrush steppe ecosystems predicted changes in climate may manifest as a shift from historically winter/snow-dominated precipitation regimes to one dominated by spring rains. In these ecosystems soil microorganisms play a vital role in linking the effects of water availability and plant productivity to biogeochemical cycling. Patterns of soil microbial catalyzed organic matter decomposition patters (i.e. patterns of extracellular enzyme activity (EEA)) are thought to depend upon the quantity and quality of soil organic matter (SOM), pH, and mean annual precipitation (Sinsabaugh, 2008), and less on the timing and magnitude of precipitation. However, sagebrush-steppe plant communities respond strongly to changes in the timing and magnitude of precipitation, and preliminary findings by our group suggest that corresponding changes in SOM quantity, quality, N-cycle dynamics, and soil structure are occurring. Therefore, we hypothesized: 1) Shifts in the timing and magnitude of precipitation would indirectly affect soil microbial decomposition patterns via responses in the plant community structure; and 2) Changes in precipitation patterns can directly affect soil microbial community structure and function, in effect uncoupling the interaction between plant community structure and soil community structure. We tested our hypotheses by determining the influence of experimentally manipulated timing and magnitude of precipitation on soil microbial EEA using standard flourometric assays in soils sampled under plant canopies and plant interspaces. We assessed this response in a mature (18 + years) ecohydrologic field experiment in eastern Idaho that annually imitates three possible post climatic-shift precipitation regimes (Ambient (AMB): no additional precipitation, ~200mm annually; Summer (SUMM): 200mm provisioned at 50mm bi-weekly starting in June; and Fall/Spring (F/S): 200mm provisioned over 1-2 weeks in October or April) (n=3). Within plant interspaces Beta glucosaminide activity increased by 18% in treatments receiving additional F/S precipitation, whereas alpha glucopyranoside activity was lower in the F/S and SUMM plots. Conversely, underplant canopies alpha glucopyranoside activity increased by 15% in the SUMM and F/S precipitation treatments. Across treatments and sampling types (i.e. plant canopy vs. interspace), cellobioside activity levels are consistently elevated in response to additional precipitation compared to those of the control plots. When coupled with recent preliminary findings by our group regarding changes in plant and microbial community structure and SOM, C-storage, and soil structural responses, these preliminary findings suggest that 1) microbial community structure and function respond both directly and indirectly to changes in climate, and 2) thus provide a mechanism for changes in plant community structure to feed-forward to affect soil carbon decomposition patterns and ultimately soil carbon storage potential.

Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer.

PubMed

van Gils, Stijn; Tamburini, Giovanni; Marini, Lorenzo; Biere, Arjen; van Agtmaal, Maaike; Tyc, Olaf; Kos, Martine; Kleijn, David; van der Putten, Wim H

2017-01-01

There is increasing evidence showing that microbes can influence plant-insect interactions. In addition, various studies have shown that aboveground pathogens can alter the interactions between plants and insects. However, little is known about the role of soil-borne pathogens in plant-insect interactions. It is also not known how environmental conditions, that steer the performance of soil-borne pathogens, might influence these microbe-plant-insect interactions. Here, we studied effects of the soil-borne pathogen Rhizoctonia solani on aphids (Sitobion avenae) using wheat (Triticum aestivum) as a host. In a greenhouse experiment, we tested how different levels of soil organic matter (SOM) and fertilizer addition influence the interactions between plants and aphids. To examine the influence of the existing soil microbiome on the pathogen effects, we used both unsterilized field soil and sterilized field soil. In unsterilized soil with low SOM content, R. solani addition had a negative effect on aphid biomass, whereas it enhanced aphid biomass in soil with high SOM content. In sterilized soil, however, aphid biomass was enhanced by R. solani addition and by high SOM content. Plant biomass was enhanced by fertilizer addition, but only when SOM content was low, or in the absence of R. solani. We conclude that belowground pathogens influence aphid performance and that the effect of soil pathogens on aphids can be more positive in the absence of a soil microbiome. This implies that experiments studying the effect of pathogens under sterile conditions might not represent realistic interactions. Moreover, pathogen-plant-aphid interactions can be more positive for aphids under high SOM conditions. We recommend that soil conditions should be taken into account in the study of microbe-plant-insect interactions.

Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations

PubMed Central

Martins, Guilherme; Lauga, Béatrice; Miot-Sertier, Cécile; Mercier, Anne; Lonvaud, Aline; Soulas, Marie-Louise; Soulas, Guy; Masneuf-Pomarède, Isabelle

2013-01-01

Despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. In this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. Analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. The highest bacteria population counts and the greatest diversity of genera were found in soil samples, followed by bark, grapes and leaves. The identification of isolates revealed that some genera – Pseudomonas, Curtobacterium, and Bacillus – were present in all ecosystems, but in different amounts, while others were ecosystem-specific. About 50% of the genera were common to soil and bark, but absent from leaves and grapes. The opposite was also observed: grape and leaf samples presented 50% of genera in common that were absent from trunk and soil. The bacterial community structure analyzed by T-RFLP indicated similarities between the profiles of leaves and grapes, on the one hand, and bark and soil, on the other, reflecting the number of shared T-RFs. The results suggest an interaction between telluric bacterial communities and the epiphytic bacteria present on the different grapevine parts. PMID:24023666

A Simplified Land Model (SLM) for use in cloud-resolving models: Formulation and evaluation

NASA Astrophysics Data System (ADS)

Lee, Jungmin M.; Khairoutdinov, Marat

2015-09-01

A Simplified Land Model (SLM) that uses a minimalist set of parameters with a single-layer vegetation and multilevel soil structure has been developed distinguishing canopy and undercanopy energy budgets. The primary motivation has been to design a land model for use in the System for Atmospheric Modeling (SAM) cloud-resolving model to study land-atmosphere interactions with a sufficient level of realism. SLM uses simplified expressions for the transport of heat, moisture, momentum, and radiation in soil-vegetation system. The SLM performance has been evaluated over several land surface types using summertime tower observations of micrometeorological and biophysical data from three AmeriFlux sites, which include grassland, cropland, and deciduous-broadleaf forest. In general, the SLM captures the observed diurnal cycle of surface energy budget and soil temperature reasonably well, although reproducing the evolution of soil moisture, especially after rain events, has been challenging. The SLM coupled to SAM has been applied to the case of summertime shallow cumulus convection over land based on the Atmospheric Radiation Measurements (ARM) Southern Great Plain (SGP) observations. The simulated surface latent and sensible heat fluxes as well as the evolution of thermodynamic profiles in convective boundary layer agree well with the estimates based on the observations. Sensitivity of atmospheric boundary layer development to the soil moisture and different land cover types has been also examined.

Adaptive management for soil ecosystem services

USGS Publications Warehouse

Birge, Hannah E.; Bevans, Rebecca A.; Allen, Craig R.; Angeler, David G.; Baer, Sara G.; Wall, Diana H.

2016-01-01

Ecosystem services provided by soil include regulation of the atmosphere and climate, primary (including agricultural) production, waste processing, decomposition, nutrient conservation, water purification, erosion control, medical resources, pest control, and disease mitigation. The simultaneous production of these multiple services arises from complex interactions among diverse aboveground and belowground communities across multiple scales. When a system is mismanaged, non-linear and persistent losses in ecosystem services can arise. Adaptive management is an approach to management designed to reduce uncertainty as management proceeds. By developing alternative hypotheses, testing these hypotheses and adjusting management in response to outcomes, managers can probe dynamic mechanistic relationships among aboveground and belowground soil system components. In doing so, soil ecosystem services can be preserved and critical ecological thresholds avoided. Here, we present an adaptive management framework designed to reduce uncertainty surrounding the soil system, even when soil ecosystem services production is not the explicit management objective, so that managers can reach their management goals without undermining soil multifunctionality or contributing to an irreversible loss of soil ecosystem services.

A long-term soil structure observatory for post-compaction soil structure evolution: design and initial soil structure recovery observations

NASA Astrophysics Data System (ADS)

Keller, Thomas; Colombi, Tino; Ruiz, Siul; Grahm, Lina; Reiser, René; Rek, Jan; Oberholzer, Hans-Rudolf; Schymanski, Stanislaus; Walter, Achim; Or, Dani

2016-04-01

Soil compaction due to agricultural vehicular traffic alters the geometrical arrangement of soil constituents, thereby modifying mechanical properties and pore spaces that affect a range of soil hydro-ecological functions. The ecological and economic costs of soil compaction are dependent on the immediate impact on soil functions during the compaction event, and a function of the recovery time. In contrast to a wealth of soil compaction information, mechanisms and rates of soil structure recovery remain largely unknown. A long-term (>10-yr) soil structure observatory (SSO) was established in 2014 on a loamy soil in Zurich, Switzerland, to quantify rates and mechanisms of structure recovery of compacted arable soil under different post-compaction management treatments. We implemented three initial compaction treatments (using a two-axle agricultural vehicle with 8 Mg wheel load): compaction of the entire plot area (i.e. track-by-track), compaction in wheel tracks, and no compaction. After compaction, we implemented four post-compaction soil management systems: bare soil (BS), permanent grass (PG), crop rotation without mechanical loosening (NT), and crop rotation under conventional tillage (CT). BS and PG provide insights into uninterrupted natural processes of soil structure regeneration under reduced (BS) and normal biological activity (PG). The two cropping systems (NT and CT) enable insights into soil structure recovery under common agricultural practices with minimal (NT) and conventional mechanical soil disturbance (CT). Observations include periodic sampling and measurements of soil physical properties, earthworm abundance, crop measures, electrical resistivity and ground penetrating radar imaging, and continuous monitoring of state variables - soil moisture, temperature, CO2 and O2 concentrations, redox potential and oxygen diffusion rates - for which a network of sensors was installed at various depths (0-1 m). Initial compaction increased soil bulk density to about half a metre, decreased gas and water transport functions (air permeability, gas diffusivity, saturated hydraulic conductivity), and increased mechanical impedance. Water infiltration at the soil surface was initially reduced by three orders of magnitude, but significantly recovered within a year. However, within the soil profile, recovery of transport properties is much smaller. Air permeability tended to recover more than gas diffusivity, suggesting that initial post-compaction recovery is initiated by new macropores (e.g. biopores). Tillage recovered topsoil bulk density but not topsoil transport functions. Compaction changed grass species composition in PG, and significantly reduced grass biomass in PG and crop yields in NT and CT.

Application of Nonlinear Seismic Soil-Structure Interaction Analysis for Identification of Seismic Margins at Nuclear Power Plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varma, Amit H.; Seo, Jungil; Coleman, Justin Leigh

2015-11-01

Seismic probabilistic risk assessment (SPRA) methods and approaches at nuclear power plants (NPP) were first developed in the 1970s and aspects of them have matured over time as they were applied and incrementally improved. SPRA provides information on risk and risk insights and allows for some accounting for uncertainty and variability. As a result, SPRA is now used as an important basis for risk-informed decision making for both new and operating NPPs in the US and in an increasing number of countries globally. SPRAs are intended to provide best estimates of the various combinations of structural and equipment failures thatmore » can lead to a seismic induced core damage event. However, in some instances the current SPRA approach contains large uncertainties, and potentially masks other important events (for instance, it was not the seismic motions that caused the Fukushima core melt events, but the tsunami ingress into the facility). INL has an advanced SPRA research and development (R&D) activity that will identify areas in the calculation process that contain significant uncertainties. One current area of focus is the use of nonlinear soil-structure interaction (NLSSI) analysis methods to accurately capture: 1) nonlinear soil behavior and 2) gapping and sliding between the NPP and soil. The goal of this study is to compare numerical NLSSI analysis results with recorded earthquake ground motions at Fukushima Daichii (Great Tohuku Earthquake) and evaluate the sources of nonlinearity contributing to the observed reduction in peak acceleration. Comparisons are made using recorded data in the free-field (soil column with no structural influence) and recorded data on the NPP basemat (in-structure response). Results presented in this study should identify areas of focus for future R&D activities with the goal of minimizing uncertainty in SPRA calculations. This is not a validation activity since there are too many sources of uncertainty that a numerical analysis would need to consider (variability in soil material properties, structural material properties, etc.). Rather the report will determine if the NLSSI calculations are following similar trends observed in the recorded data (i.e. reductions in maximum acceleration between the free-field and basemat) Numerical NLSSI results presented show maximum accelerations between the free field and basemat were reduced the EW and NS directions. The maximum acceleration in the UD direction increased slightly. The largest reduction in maximum accelerations between the modeled free-field and the NPP basemat resulted in nearly 50% reduction. The observation in reduction of numerical maximum accelerations in the EW and NS directions follows the observed trend in the recorded data. The maximum reductions observed in these NLSSI studies were due to soil nonlinearities, not gapping and sliding (although additional R&D is needed to develop an appropriate approach to model gapping and sliding). This exploratory study highlights the need for additional R&D on developing: (i) improved modeling of soil nonlinearities (soil constitutive models that appropriately capture cyclic soil behavior), (ii) improved modeling of gapping and sliding at the soil-structure interface (to appropriately capture the dissipation of energy at this interface), and (iii) experimental laboratory test data to calibrate the items (i) and (ii).« less

Influence of management history and landscape variables on soil organic carbon and soil redistribution

USGS Publications Warehouse

Venteris, E.R.; McCarty, G.W.; Ritchie, J.C.; Gish, T.

2004-01-01

Controlled studies to investigate the interaction between crop growth, soil properties, hydrology, and management practices are common in agronomy. These sites (much as with real world farmland) often have complex management histories and topographic variability that must be considered. In 1993 an interdisiplinary study was started for a 20-ha site in Beltsville, MD. Soil cores (271) were collected in 1999 in a 30-m grid (with 5-m nesting) and analyzed as part of the site characterization. Soil organic carbon (SOC) and 137Cesium (137Cs) were measured. Analysis of aerial photography from 1992 and of farm management records revealed that part of the site had been maintained as a swine pasture and the other portion as cropped land. Soil properties, particularly soil redistribution and SOC, show large differences in mean values between the two areas. Mass C is 0.8 kg m -2 greater in the pasture area than in the cropped portion. The pasture area is primarily a deposition site, whereas the crop area is dominated by erosion. Management influence is suggested, but topographic variability confounds interpretation. Soil organic carbon is spatially structured, with a regionalized variable of 120 m. 137Cs activity lacks spatial structure, suggesting disturbance of the profile by animal activity and past structures such as swine shelters and roads. Neither SOC nor 137Cs were strongly correlated to terrain parameters, crop yields, or a seasonal soil moisture index predicted from crop yields. SOC and 137Cs were weakly correlated (r2 ???0.2, F-test P-value 0.001), suggesting that soil transport controls, in part, SOC distribution. The study illustrates the importance of past site history when interpreting the landscape distribution of soil properties, especially those strongly influenced by human activity. Confounding variables, complex soil hydrology, and incomplete documentation of land use history make definitive interpretations of the processes behind the spatial distributions difficult. Such complexity may limit the accuracy of scaling approaches to mapping SOC and soil redistribution.

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

PubMed Central

Lladó, Salvador; López-Mondéjar, Rubén

2017-01-01

SUMMARY The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously. PMID:28404790

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change.

PubMed

Lladó, Salvador; López-Mondéjar, Rubén; Baldrian, Petr

2017-06-01

The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously. Copyright © 2017 American Society for Microbiology.

Long-Term Uptake of Phenol-Water Vapor Follows Similar Sigmoid Kinetics on Prehydrated Organic Matter- and Clay-Rich Soil Sorbents.

PubMed

Borisover, Mikhail; Bukhanovsky, Nadezhda; Lado, Marcos

2017-09-19

Typical experimental time frames allowed for equilibrating water-organic vapors with soil sorbents might lead to overlooking slow chemical reactions finally controlling a thermodynamically stable state. In this work, long-term gravimetric examination of kinetics covering about 4000 h was performed for phenol-water vapor interacting with four materials pre-equilibrated at three levels of air relative humidity (RHs 52, 73, and 92%). The four contrasting sorbents included an organic matter (OM)-rich peat soil, an OM-poor clay soil, a hydrophilic Aldrich humic acid salt, and water-insoluble leonardite. Monitoring phenol-water vapor interactions with the prehydrated sorbents, as compared with the sorbent samples in phenol-free atmosphere at the same RH, showed, for the first time, a sigmoid kinetics of phenol-induced mass uptake typical for second-order autocatalytic reactions. The apparent rate constants were similar for all the sorbents, RHs and phenol activities studied. A significant part of sorbed phenol resisted extraction, which was attributed to its abiotic oxidative coupling. Phenol uptake by peat and clay soils was also associated with a significant enhancement of water retention. The delayed development of the sigmoidal kinetics in phenol-water uptake demonstrates that long-run abiotic interactions of water-organic vapor with soil may be overlooked, based on short-term examination.

A multi-omics and imaging approach to understand soil organic matter composition and its interaction with microbes.

NASA Astrophysics Data System (ADS)

Tfaily, M. M.; Walker, L. R.; Kyle, J. E.; Chu, R. K.; Dohnalkova, A.; Tolic, N.; Orton, D.; Robinson, E. R.; Paša-Tolić, L.; Hess, N. J.

2015-12-01

The focus on soil C dynamics is currently relevant as researchers and policymakers strive to understand the feedbacks between ecosystem stress and climate change. Successful development of molecular profiles that link soil microbiology with soil carbon (C) dynamics to ascertain soil vulnerability and resilience to climate change would have great impact on assessments of soil ecosystems in response to climate change. Additionally, a better understanding of the soil C dynamics would improve climate modeling, and fate and transport of carbon across terrestrial, subsurface and atmospheric interfaces. Unravelling the wide range of possible interactions between and within the microbial communities, with minerals and organic compounds in the terrestrial ecosystem requires a multimodal, molecular approach. Here we report on the use of a combination of several molecular 'omics' approaches: metabolomics, metallomics, lipidomics, and proteomics coupled with a suite of high resolution imaging, and X-ray diffraction crystallographic techniques, as a novel methodology to understand SOM composition, and its interaction with microbial communities in different ecosystems, including C associated with mineral surfaces. The findings of these studies provide insights into the SOM persistence and microbial stabilization of carbon in ecosystems and reveal the powerful coupling of a multi-scale of techniques. Examples of this approach will be presented from field studies of simulated climate change, and laboratory column-grown Pinus resinosa mesocosms.

Fate and Transport of Nanoparticles in Porous Media: A Numerical Study

NASA Astrophysics Data System (ADS)

Taghavy, Amir

Understanding the transport characteristics of NPs in natural soil systems is essential to revealing their potential impact on the food chain and groundwater. In addition, many nanotechnology-based remedial measures require effective transport of NPs through soil, which necessitates accurate understanding of their transport and retention behavior. Based upon the conceptual knowledge of environmental behavior of NPs, mathematical models can be developed to represent the coupling of processes that govern the fate of NPs in subsurface, serving as effective tools for risk assessment and/or design of remedial strategies. This work presents an innovative hybrid Eulerian-Lagrangian modeling technique for simulating the simultaneous reactive transport of nanoparticles (NPs) and dissolved constituents in porous media. Governing mechanisms considered in the conceptual model include particle-soil grain, particle-particle, particle-dissolved constituents, and particle- oil/water interface interactions. The main advantage of this technique, compared to conventional Eulerian models, lies in its ability to address non-uniformity in physicochemical particle characteristics. The developed numerical simulator was applied to investigate the fate and transport of NPs in a number of practical problems relevant to the subsurface environment. These problems included: (1) reductive dechlorination of chlorinated solvents by zero-valent iron nanoparticles (nZVI) in dense non-aqueous phase liquid (DNAPL) source zones; (2) reactive transport of dissolving silver nanoparticles (nAg) and the dissolved silver ions; (3) particle-particle interactions and their effects on the particle-soil grain interactions; and (4) influence of particle-oil/water interface interactions on NP transport in porous media.

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.

PubMed

Flores-Rentería, Dulce; Curiel Yuste, Jorge; Rincón, Ana; Brearley, Francis Q; García-Gil, Juan Carlos; Valladares, Fernando

2015-05-01

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

PubMed Central

Gałązka, Anna; Grządziel, Jarosław

2018-01-01

Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS), reduced tillage (RT), full tillage (FT), and crop rotation (CR). Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation) and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation). The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895), genus level (P = 0.026, F = 3.313) and on the species level (P = 0.033, F = 2.718). This study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function. PMID:29441054

Small-scale spatial variability in phylogenetic community structure during early plant succession depends on soil properties.

PubMed

Ulrich, Werner; Piwczyński, Marcin; Zaplata, Markus Klemens; Winter, Susanne; Schaaf, Wolfgang; Fischer, Anton

2014-07-01

During early plant succession, the phylogenetic structure of a community changes in response to important environmental filters and emerging species interactions. We traced the development of temperate-zone plant communities during the first 7 years of primary succession on catchment soils to explore patterns of initial species assembly. We found pronounced small-scale differences in the phylogenetic composition of neighbouring plant assemblages and a large-scale trend towards phylogenetic evenness. This small-scale variability appears to be mediated by soil properties, particularly carbonate content. Therefore, abiotic environmental conditions might counteract or even supersede the effects of interspecific competition among closely related species, which are usually predicted to exhibit patterns of phylogenetic evenness. We conclude that theories on phylogenetic community composition need to incorporate effects of small-scale variability of environmental factors.

How do soil physical conditions for crop growth vary over time under established contrasting tillage regimes?

NASA Astrophysics Data System (ADS)

Hallett, Paul; Stobart, Ron; Valentine, Tracy; George, Timothy; Morris, Nathan; Newton, Adrian; McKenzie, Blair

2014-05-01

When plant breeders develop modern cereal varieties for the sustainable intensification of agriculture, insufficient thought is given to the impact of tillage on soil physical conditions for crop production. In earlier work, we demonstrated that barley varieties that perform best in ploughed soil (the approach traditionally used for breeding trials) were not the same as those performing best under shallow non-inversion or zero-tillage. We also found that the Quantitative Trait Loci (QTL) associated with improved phosphorus uptake, and hence useful for marker assisted breeding, were not robust between different tillage regimes. The impact of the soil environment had greater impact than the genetics in GxE interactions. It is obvious that soil tillage should be considered when breeding the next generation of crops. Tillage may also have important impacts on carbon storage, but we found that despite greater soil carbon at shallow depths under non-inversion tillage, the carbon stored throughout the soil profile was not affected by tillage. Studies on soil tillage impacts to crop productivity and soil quality are often performed in one season, on single sites that have had insufficient time to develop. Our current research explores multiple sites, on different soils, with temporal measurements of soil physical conditions under contrasting tillage regimes. We use the oldest established contemporary tillage experiments in the United Kingdom, with all sites sharing ploughed and shallow (7cm) non-inversion tillage treatments. In eastern Scotland (Mid Pilmore), the site also has zero tillage and deep ploughing (40 cm) treatments, and was established 11 years ago. In east England there are two sites, both also having a deep non-inversion tillage treatment, and they were established 6 (New Farm Systems) and 8 (STAR) years ago. We measure a range of crop and soil properties at sowing, one month after sowing and post-harvest, including rapid lab based assays that allow high-throughput. Samples are taken over the rooting zone in the topsoil, plough pan and subsoil. The first year's dataset from this comprehensive project will be presented. Early data identified plough pans under shallow non-inversion tillage that will limit root growth at all sites. Aggregate stabilities vary as expected, with plough soils at shallow depth being less stable than non-inversion tillage, but greater stability in plough soils at greater depth due to incorporated organic matter. Very rapidly following cultivation, the seedbeds coalesce, resulting in a more challenging physical environment for crop growth. We are exploring the mechanisms in soil structure temporal dynamics in greater detail, including the resilience of seedbeds to structural degradation through natural weathering and the action of plants. These profound differences in soil conditions will impact the root ideotype of crops for these different conditions. This has implications for the way in which breeding and genotype selection is performed in the future. Ultimately, we aim to identify crop varieties suited to local soil conditions and management, possibly with root traits that boost yields and soil physical quality.

Arctic Tundra Soils: A Microbial Feast That Shrubs Will Cease

NASA Astrophysics Data System (ADS)

Machmuller, M.; Calderon, F.; Cotrufo, M. F.; Lynch, L.; Paul, E. A.; Wallenstein, M. D.

2016-12-01

Rapid climate warming may already be driving rapid decomposition of the vast stocks of carbon in Arctic tundra soils. However, stimulated decomposition may also release nitrogen and support increased plant productivity, potentially counteracting soil carbon losses. At the same time, these two processes interact, with plant derived carbon potentially fueling soil microbes to attack soil organic matter (SOM) to acquire nitrogen- a process known as priming. Thus, differences in the physiology, stoichiometry and microbial interactions among plant species could affect climate-carbon feedbacks. To reconcile these interactive mechanisms, we examined how vegetation type (Betula nana and Eriophorum vaginatum) and fertilization (short-term and long-term) influenced the decomposition of native SOM after labile carbon and nutrient addition. We hypothesized that labile carbon inputs would stimulate the loss of native SOM, but the magnitude of this effect would be indirectly related to soil nitrogen concentrations (e.g. SOM priming would be highest in N-limited soils). We added isotopically enriched (13C) glucose and ammonium nitrate to soils under shrub (B. nana) and tussock (E. vaginatum) vegetation. We found that nitrogen additions stimulated priming only in tussock soils, characterized by lower nutrient concentrations and microbial biomass (p<0.05). There was no evidence of priming in soils that had been fertilized for >20yrs. Rather, we found that long-term fertilization shifted SOM chemistry towards a greater abundance of recalcitrant SOM, lower microbial biomass, and decreased SOM respiration (p<0.05). Our results suggest that, in the short-term, the magnitude of SOM priming is dependent on vegetation and soil nitrogen concentrations, but this effect may not persist if shrubs increase in abundance under climate warming. Therefore, including nitrogen as a control on SOM decomposition and priming is critical to accurately model the effects of climate change on arctic carbon storage.

Physiological and biochemical perspectives of non-salt tolerant plants during bacterial interaction against soil salinity.

PubMed

Radhakrishnan, Ramalingam; Baek, Kwang Hyun

2017-07-01

Climatic changes on earth affect the soil quality of agricultural lands, especially by increasing salt deposition in soil, which results in soil salinity. Soil salinity is a major challenge to growth and reproduction among glycophytes (including all crop plants). Soil bacteria present in the rhizosphere and/or roots naturally protect plants from the adverse effects of soil salinity by reprogramming the stress-induced physiological changes in plants. Bacteria can enrich the soil with major nutrients (nitrogen, phosphorus, and potassium) in a form easily available to plants and prevent the transport of excess sodium to roots (exopolysaccharides secreted by bacteria bind with sodium ions) for maintaining ionic balance and water potential in cells. Salinity also affects plant growth regulators and suppresses seed germination and root and shoot growth. Bacterial secretion of indole-3-acetic acid and gibberellins compensates for the salt-induced hormonal decrease in plants, and bacterial 1-aminocyclopropane-1-carboxylate (ACC) deaminase synthesis decreases ethylene production to stimulate plant growth. Furthermore, bacteria modulate the redox state of salinity-affected plants by enhancing antioxidants and polyamines, which leads to increased photosynthetic efficiency. Bacteria-induced accumulation of compatible solutes in stressed plants regulates plant cellular activities and prevents salt stress damage. Plant-bacterial interaction reprograms the expression of salt stress-responsive genes and proteins in salinity-affected plants, resulting in a precise stress mitigation metabolism as a defense mechanism. Soil bacteria increase the fertility of soil and regulate the plant functions to prevent the salinity effects in glycophytes. This review explains the current understanding about the physiological changes induced in glycophytes during bacterial interaction to alleviate the adverse effects of soil salinity stress. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Diel hysteresis between soil respiration and soil temperature in a biological soil crust covered desert ecosystem

PubMed Central

Li, Xinrong; Zhang, Peng; Chen, Yongle

2018-01-01

Soil respiration induced by biological soil crusts (BSCs) is an important process in the carbon (C) cycle in arid and semi-arid ecosystems, where vascular plants are restricted by the harsh environment, particularly the limited soil moisture. However, the interaction between temperature and soil respiration remains uncertain because of the number of factors that control soil respiration, including temperature and soil moisture, especially in BSC-dominated areas. In this study, the soil respiration in moss-dominated crusts and lichen-dominated crusts was continuously measured using an automated soil respiration system over a one-year period from November 2015 to October 2016 in the Shapotou region of the Tengger Desert, northern China. The results indicated that over daily cycles, the half-hourly soil respiration rates in both types of BSC-covered areas were commonly related to the soil temperature. The observed diel hysteresis between the half-hourly soil respiration rates and soil temperature in the BSC-covered areas was limited by nonlinearity loops with semielliptical shapes, and soil temperature often peaked later than the half-hourly soil respiration rates in the BSC-covered areas. The average lag times between the half-hourly soil respiration rates and soil temperature for both types of BSC-covered areas were two hours over the diel cycles, and they were negatively and linearly related to the volumetric soil water content. Our results highlight the diel hysteresis phenomenon that occurs between soil respiration rates and soil temperatures in BSC-covered areas and the negative response of this phenomenon to soil moisture, which may influence total C budget evaluations. Therefore, the interactive effects of soil temperature and moisture on soil respiration in BSC-covered areas should be considered in global carbon cycle models of desert ecosystems. PMID:29624606

Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence.

PubMed

Schimann, Heidy; Bach, Cyrille; Lengelle, Juliette; Louisanna, Eliane; Barantal, Sandra; Murat, Claude; Buée, Marc

2017-02-01

The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.

Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem

PubMed Central

He, Zhili; Xiong, Jinbo; Kent, Angela D; Deng, Ye; Xue, Kai; Wang, Gejiao; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2014-01-01

The concentrations of atmospheric carbon dioxide (CO2) and tropospheric ozone (O3) have been rising due to human activities. However, little is known about how such increases influence soil microbial communities. We hypothesized that elevated CO2 (eCO2) and elevated O3 (eO3) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. To test these hypotheses, we analyzed 96 soil samples from a soybean free-air CO2 enrichment (SoyFACE) experimental site using a comprehensive functional gene microarray (GeoChip 3.0). The results showed the overall functional composition and structure of soil microbial communities shifted under eCO2, eO3 or eCO2+eO3. Key functional genes involved in carbon fixation and degradation, nitrogen fixation, denitrification and methane metabolism were stimulated under eCO2, whereas those involved in N fixation, denitrification and N mineralization were suppressed under eO3, resulting in the fact that the abundance of some eO3-supressed genes was promoted to ambient, or eCO2-induced levels by the interaction of eCO2+eO3. Such effects appeared distinct for each treatment and significantly correlated with soil properties and soybean yield. Overall, our analysis suggests possible mechanisms of microbial responses to global atmospheric change factors through the stimulation of C and N cycling by eCO2, the inhibition of N functional processes by eO3 and the interaction by eCO2 and eO3. This study provides new insights into our understanding of microbial functional processes in response to global atmospheric change in soybean agro-ecosystems. PMID:24108327

Development of Soils and Communities of Plants and Arbuscular Mycorrhizal Fungi on West Virginia Surface Mines

NASA Astrophysics Data System (ADS)

Levy, Michael A.; Cumming, Jonathan R.

2014-11-01

Surface mining followed by reclamation to pasture is a major driver of land use and cover change in Appalachia. Prior research suggests that many aspects of ecosystem recovery are either slow or incomplete. We examined ecosystem structure—including soil physical and chemical properties, arbuscular mycorrhizal fungal (AMF) infectivity and community composition, and plant diversity and community composition—on a chronosequence of pasture-reclaimed surface mines and a non-mined pasture in northern West Virginia. Surface mining and reclamation dramatically altered ecosystem structure. Some aspects of ecosystem structure, including many measures of soil chemistry and infectivity of AMF, returned rapidly to levels found on the non-mined reference site. Other aspects of ecosystem structure, notably soil physical properties and AMF and plant communities, showed incomplete or no recovery over the short-to-medium term. In addition, invasive plants were prevalent on reclaimed mine sites. The results point to the need for investigation on how reclamation practices could minimize establishment of exotic invasive plant species and reduce the long-term impacts of mining on ecosystem structure and function.

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere. X-ray Computed Tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and in-house developed code was used to non-invasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure, and extract quantitative information from the 3D data, respectively. Based on the explicitly-resolved root structure, pore-scale computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soilmore » hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. Furthermore, the coupled imaging-modeling approach demonstrates a realistic platform to investigate rhizosphere flow processes and would be feasible to provide useful information linked to upscaled models.« less

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

DOE PAGES

Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan; ...

2017-05-04

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere. X-ray Computed Tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and in-house developed code was used to non-invasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure, and extract quantitative information from the 3D data, respectively. Based on the explicitly-resolved root structure, pore-scale computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soilmore » hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. Furthermore, the coupled imaging-modeling approach demonstrates a realistic platform to investigate rhizosphere flow processes and would be feasible to provide useful information linked to upscaled models.« less

Soil microbial community successional patterns during forest ecosystem restoration.

PubMed

Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

PubMed Central

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

Coupled Modeling of Rhizosphere and Reactive Transport Processes

NASA Astrophysics Data System (ADS)

Roque-Malo, S.; Kumar, P.

2017-12-01

The rhizosphere, as a bio-diverse plant root-soil interface, hosts many hydrologic and biochemical processes, including nutrient cycling, hydraulic redistribution, and soil carbon dynamics among others. The biogeochemical function of root networks, including the facilitation of nutrient cycling through absorption and rhizodeposition, interaction with micro-organisms and fungi, contribution to biomass, etc., plays an important role in myriad Critical Zone processes. Despite this knowledge, the role of the rhizosphere on watershed-scale ecohydrologic functions in the Critical Zone has not been fully characterized, and specifically, the extensive capabilities of reactive transport models (RTMs) have not been applied to these hydrobiogeochemical dynamics. This study uniquely links rhizospheric processes with reactive transport modeling to couple soil biogeochemistry, biological processes, hydrologic flow, hydraulic redistribution, and vegetation dynamics. Key factors in the novel modeling approach are: (i) bi-directional effects of root-soil interaction, such as simultaneous root exudation and nutrient absorption; (ii) multi-state biomass fractions in soil (i.e. living, dormant, and dead biological and root materials); (iii) expression of three-dimensional fluxes to represent both vertical and lateral interconnected flows and processes; and (iv) the potential to include the influence of non-stationary external forcing and climatic factors. We anticipate that the resulting model will demonstrate the extensive effects of plant root dynamics on ecohydrologic functions at the watershed scale and will ultimately contribute to a better characterization of efflux from both agricultural and natural systems.

Weaker soil carbon-climate feedbacks resulting from microbial and abiotic interactions

NASA Astrophysics Data System (ADS)

Tang, Jinyun; Riley, William J.

2015-01-01

The large uncertainty in soil carbon-climate feedback predictions has been attributed to the incorrect parameterization of decomposition temperature sensitivity (Q10; ref. ) and microbial carbon use efficiency. Empirical experiments have found that these parameters vary spatiotemporally, but such variability is not included in current ecosystem models. Here we use a thermodynamically based decomposition model to test the hypothesis that this observed variability arises from interactions between temperature, microbial biogeochemistry, and mineral surface sorptive reactions. We show that because mineral surfaces interact with substrates, enzymes and microbes, both Q10 and microbial carbon use efficiency are hysteretic (so that neither can be represented by a single static function) and the conventional labile and recalcitrant substrate characterization with static temperature sensitivity is flawed. In a 4-K temperature perturbation experiment, our fully dynamic model predicted more variable but weaker soil carbon-climate feedbacks than did the static Q10 and static carbon use efficiency model when forced with yearly, daily and hourly variable temperatures. These results imply that current Earth system models probably overestimate the response of soil carbon stocks to global warming. Future ecosystem models should therefore consider the dynamic interactions between sorptive mineral surfaces, substrates and microbial processes.

The World Soil Museum: education and advocacy on soils of the world

NASA Astrophysics Data System (ADS)

Mantel, Stephan; Land, Hiske

2013-04-01

The World Soil Museum (WSM) in Wageningen, is part of ISRIC World Soil Information and was founded in 1966 on request of the United Nations Educational, Scientific and Cultural Organization (UNESCO) and the International Soil Science Society. The World Soil Museum has a collection of over 1100 soil profiles from more than 70 countries. This soil profiles are vertical sections and show the composition, layering and structure of the soil. The collection is unique in the world and includes a significant number of soil profiles from the Netherlands. The Dutch soil collection is important for serving broader visitor groups, as some visitors, such as secondary school classes, are specifically interested in the Dutch landscape and soils. Broadly speaking, the World Soil Museum has five functions: (i) education and courses, (ii) research, (iii) information and edutainment, (iv) social function, and (v) a real museum function (Art). The World Soil Museum (World Soil Museum) is well known in national and international circles soil and the English name has almost 1,000 references on the Internet. The World Soil Museum is visited by about 1000 people a year, mainly university and college students from Western Europe. Other visitor groups that have found their way to the museum are students from disciplines broader then soil science, such as geography and rural development. Secondary school classes visit the museum for geography classes. The uniqueness and the value of the collection of soil profiles (soil monoliths) and associated collections, such as soil samples, hand pieces, thin sections, slides, is emphasized by the fact ISRIC is the only World Data Centre for Soils (WDC-Soils) within the World Data System of the International Council of Science (ICSU). The collection provides an insight in and overview of the diversity of soils in the world, their properties and their limitations and possibilities for use. A new building is under construction for the WSM, which is expected to be ready mid-2013. The location is appropriately placed on the Wageningen University Campus, close to the students and research centres of the University. The new exposition space will provide new opportunities for serving different visitor groups. The selection of about 80 soil monoliths representing the world's soils will be maintained in the new exposition. In addition, interactive displays will support education. A circular, interactive map of the world will be placed centrally in the exposition and will serve as a portal to the soil information. The map data refer to the monoliths on the walls and vice versa. Around the central map six theme stations communicate current topics that show the relevance of soil in different fields. For the general public it will explain the principles of soil formation and it will show the relevance to actual issues like food production and climate change. High school students in their final years can come here for work assignments and orientation days. Academic students and scientists, from both the Netherlands and other (mainly) northern European countries can continue to come to the WSM for education, study and research.

Soil formation: Chapter 6

USGS Publications Warehouse

Goldhaber, Martin B.; Banwart, Steven A.

2015-01-01

Soil formation reflects the complex interaction of many factors, among the most important of which are (i) the nature of the soil parent material, (ii) regional climate, (iii) organisms, including humans, (iv) topography and (v) time. These processes operate in Earth's critical zone; the thin veneer of our planet where rock meets life. Understanding the operation of these soil-forming factors requires an interdisciplinary approach and is a necessary predicate to charactering soil processes and functions, mitigating soil degradation and adapting soil management to environmental change. In this chapter, we discuss how these soil-forming factors operate both singly and in concert in natural and human modified environments. We emphasize the role that soil organic matter plays in these processes to provide context for understanding the benefits that it bestows on humanity.

Ecological strategies in california chaparral: Interacting effects of soils, climate, and fire on specific leaf area

USGS Publications Warehouse

Anacker, Brian; Rajakaruna, Nishanta; Ackerly, David; Harrison, Susan; Keeley, Jon E.; Vasey, Michael

2011-01-01

Background: High values of specific leaf area (SLA) are generally associated with high maximal growth rates in resource-rich conditions, such as mesic climates and fertile soils. However, fire may complicate this relationship since its frequency varies with both climate and soil fertility, and fire frequency selects for regeneration strategies (resprouting versus seeding) that are not independent of resource-acquisition strategies. Shared ancestry is also expected to affect the distribution of resource-use and regeneration traits.Aims: We examined climate, soil, and fire as drivers of community-level variation in a key functional trait, SLA, in chaparral in California.Methods: We quantified the phylogenetic, functional, and environmental non-independence of key traits for 87 species in 115 plots.Results: Among species, SLA was higher in resprouters than seeders, although not after phylogeny correction. Among communities, mean SLA was lower in harsh interior climates, but in these climates it was higher on more fertile soils and on more recently burned sites; in mesic coastal climates, mean SLA was uniformly high despite variation in soil fertility and fire history.Conclusions: We conclude that because important correlations exist among both species traits and environmental filters, interpreting the functional and phylogenetic structure of communities may require an understanding of complex interactive effects.

Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions.

PubMed

Gebremikael, Mesfin T; Steel, Hanne; Buchan, David; Bert, Wim; De Neve, Stefaan

2016-09-08

The role of soil fauna in crucial ecosystem services such as nutrient cycling remains poorly quantified, mainly because of the overly reductionistic approach adopted in most experimental studies. Given that increasing nitrogen inputs in various ecosystems influence the structure and functioning of soil microbes and the activity of fauna, we aimed to quantify the role of the entire soil nematode community in nutrient mineralization in an experimental set-up emulating nutrient-rich field conditions and accounting for crucial interactions amongst the soil microbial communities and plants. To this end, we reconstructed a complex soil foodweb in mesocosms that comprised largely undisturbed native microflora and the entire nematode community added into defaunated soil, planted with Lolium perenne as a model plant, and amended with fresh grass-clover residues. We determined N and P availability and plant uptake, plant biomass and abundance and structure of the microbial and nematode communities during a three-month incubation. The presence of nematodes significantly increased plant biomass production (+9%), net N (+25%) and net P (+23%) availability compared to their absence, demonstrating that nematodes link below- and above-ground processes, primarily through increasing nutrient availability. The experimental set-up presented allows to realistically quantify the crucial ecosystem services provided by the soil biota.

Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions

NASA Astrophysics Data System (ADS)

Gebremikael, Mesfin T.; Steel, Hanne; Buchan, David; Bert, Wim; de Neve, Stefaan

2016-09-01

The role of soil fauna in crucial ecosystem services such as nutrient cycling remains poorly quantified, mainly because of the overly reductionistic approach adopted in most experimental studies. Given that increasing nitrogen inputs in various ecosystems influence the structure and functioning of soil microbes and the activity of fauna, we aimed to quantify the role of the entire soil nematode community in nutrient mineralization in an experimental set-up emulating nutrient-rich field conditions and accounting for crucial interactions amongst the soil microbial communities and plants. To this end, we reconstructed a complex soil foodweb in mesocosms that comprised largely undisturbed native microflora and the entire nematode community added into defaunated soil, planted with Lolium perenne as a model plant, and amended with fresh grass-clover residues. We determined N and P availability and plant uptake, plant biomass and abundance and structure of the microbial and nematode communities during a three-month incubation. The presence of nematodes significantly increased plant biomass production (+9%), net N (+25%) and net P (+23%) availability compared to their absence, demonstrating that nematodes link below- and above-ground processes, primarily through increasing nutrient availability. The experimental set-up presented allows to realistically quantify the crucial ecosystem services provided by the soil biota.

Forecasting the forest and the trees: consequences of drought in competitive forests

NASA Astrophysics Data System (ADS)

Clark, J. S.

2015-12-01

Models that translate individual tree responses to distribution and abundance of competing populations are needed to understand forest vulnerability to drought. Currently, biodiversity predictions rely on one scale or the other, but do not combine them. Synthesis is accomplished here by modeling data together, each with their respective scale-dependent connections to the scale needed for prediction—landscape to regional biodiversity. The approach we summarize integrates three scales, i) individual growth, reproduction, and survival, ii) size-species structure of stands, and iii) regional forest biomass. Data include 24,347 USDA Forest Inventory and Analysis (FIA) plots and 135 Long-term Forest Demography plots. Climate, soil moisture, and competitive interactions are predictors. We infer and predict the four-dimensional size/species/space/time (SSST) structure of forests, where all demographic rates respond to winter temperature, growing season length, moisture deficits, local moisture status, and competition. Responses to soil moisture are highly non-linear and not strongly related to responses to climatic moisture deficits over time. In the Southeast the species that are most sensitive to drought on dry sites are not the same as those that are most sensitive on moist sites. Those that respond most to spatial moisture gradients are not the same as those that respond most to regional moisture deficits. There is little evidence of simple tradeoffs in responses. Direct responses to climate constrain the ranges of few tree species, north or south; there is little evidence that range limits are defined by fecundity or survival responses to climate. By contrast, recruitment and the interactions between competition and drought that affect growth and survival are predicted to limit ranges of many species. Taken together, results suggest a rich interaction involving demographic responses at all size classes to neighbors, landscape variation in moisture, and regional climate change.

Lung Epithelial Healing: A Modified Seed and Soil Concept

PubMed Central

Brechbuhl, Heather M.; Smith, Mary Kathryn; Smith, Russell W.; Ghosh, Moumita

2012-01-01

Airway epithelial healing is defined as restoration of health or soundness; to cure. Our research indicates that two types of progenitor cells participate in this process: the tissue-specific stem cell (TSC) and the facultative basal progenitor (FBP). The TSC restores the epithelium to its normal structure and function. Thus, the TSC regenerates the epithelium. In contrast, the FBP-derived epithelium is characterized by regions of cellular hyperplasia and hypoplasia. Since the FBP-derived epithelium deviates from normal, we term the FBP-mediated process repair. Our work indicates that the TSC responds to signals from other epithelial cells, including the FBP. These signals instruct the TSC to proliferate or to select one of several differentiation pathways. We interpret these data in the context of Stephen Padget’s “seed and soil” paradigm. Therein, Padget explained that metastasis of a tumor, the seed, to a specific site, the soil, was determined by the growth and differentiation requirements of the tumor cell. By extending the seed and soil paradigm to airway epithelial healing, we suggest that proliferation and differentiation of the TSC, the seed, is determined by its interactions with other cell types, the soil. Based on this concept, we provide a set of suggestions for development of cell-based therapies that are directed toward chronic airways disease. PMID:22550238

Hydropedology – The last decade and the next decade

USDA-ARS?s Scientific Manuscript database

Hydropedology is an emerging interdisciplinary science that studies interactive pedologic and hydrologic processes and properties in the Earth’s Critical Zone. It emphasizes in-situ soils in the landscape, where distinct pedogenic features (e.g., structure, macropore, and horizonation), environmenta...

Excavation-caused extra deformation of existing masonry residence in soft soil region

NASA Astrophysics Data System (ADS)

Tang, Y.; Franceschelli, S.

2017-04-01

Growing need for construction of infrastructures and buildings in fast urbanization process creates challenges of interaction between buildings under construction and adjacent existing buildings. This paper presents the mitigation of contradiction between two parties who are involved the interaction using civil engineering techniques. Through the in-depth analysis of the results of monitoring surveys and enhanced accuracy and reliability of surveys, a better understanding of the behavior of deformable buildings is achieved. Combination with the original construction documents, the two parties agree that both of them are responsible for building damages and a better understanding for the rehabilitation of the existing buildings is focused on. Two cases studies are used to demonstrate and describe the importance of better understanding of the behavior of existing buildings and their rehabilitations. The objective of this study is to insight into mechanisms of soil-structure interaction for buildings adjacent to deep excavations, which can result in a damage in existing masonry residence, and to take the optimized measures to make deep excavations safety and economic and adjacent buildings keep good serviceability in urban areas with soft soil conditions.

Soil-vegetation interaction on slopes with shrub encroachment in the central Alps - simple measurements for complex slopes?

NASA Astrophysics Data System (ADS)

Caviezel, Chatrina; Hunziker, Matthias; Kuhn, Nikolaus J.

2013-04-01

In the European Alps many high mountain grasslands which where traditionally used for summer pasturing and haying have been abandoned during the last decades. Abandonment of mown or grazed grasslands causes a shift in vegetation composition, e.g. a change in landscape ecology and geomorphology. From a short term perspective, alpine areas are very fragile ecosystems and are highly sensitive to changing environmental conditions. Land use change can affect runoff and water erosion rates, snow gliding and avalanches as well as mass wasting in high-energy mountain environments. The effect of land use intensification on surface processes is well documented. However, the effect of land abandonment on surface resistance to eroding processes is discussed controversially in literature, particularly in relation to its short term and long-term consequences. Generally, perennial vegetation is considered to improve the mechanical anchoring of loose surface material and the regulation of the soil water budget including the control over the generation of runoff. This study aimed at determining the effect of green alder encroachment in the Unteralpvalley in the Swiss Alps. A range of measurements of the mechanical strength of the soil under green alder stands ranging from 15 to 90 years of age and a control site still used for grazing were conducted. Unlike the literature on the effects of perennial vegetation suggest, the data presented in this study show that soil shear strength is decreasing with along the sampled chronosequence, including compared to the grazed reference site. A possible explanation for this decline in soil stability with shrub encroachment is the loosing effect of the green alder roots on the soil structure, which causes an increase in porosity and thus less friction between soil particles. As a consequence, rates of water erosion may decline with shrub encroachment, but frequency of creeping and sliding may increase.

Estimating Grass-Soil Bioconcentration of Munitions Compounds from Molecular Structure.

PubMed

Torralba Sanchez, Tifany L; Liang, Yuzhen; Di Toro, Dominic M

2017-10-03

A partitioning-based model is presented to estimate the bioconcentration of five munitions compounds and two munition-like compounds in grasses. The model uses polyparameter linear free energy relationships (pp-LFERs) to estimate the partition coefficients between soil organic carbon and interstitial water and between interstitial water and the plant cuticle, a lipid-like plant component. Inputs for the pp-LFERs are a set of numerical descriptors computed from molecular structure only that characterize the molecular properties that determine the interaction with soil organic carbon, interstitial water, and plant cuticle. The model is validated by predicting concentrations measured in the whole plant during independent uptake experiments with a root-mean-square error (log predicted plant concentration-log observed plant concentration) of 0.429. This highlights the dominant role of partitioning between the exposure medium and the plant cuticle in the bioconcentration of these compounds. The pp-LFERs can be used to assess the environmental risk of munitions compounds and munition-like compounds using only their molecular structure as input.

Impact of treated wastewater on growth, respiration and hydraulic conductivity of citrus root systems in light and heavy soils.

PubMed

Paudel, Indira; Cohen, Shabtai; Shaviv, Avi; Bar-Tal, Asher; Bernstein, Nirit; Heuer, Bruria; Ephrath, Jhonathan

2016-06-01

Roots interact with soil properties and irrigation water quality leading to changes in root growth, structure and function. We studied these interactions in an orchard and in lysimeters with clay and sandy loam soils. Minirhizotron imaging and manual sampling showed that root growth was three times lower in the clay relative to sandy loam soil. Treated wastewater (TWW) led to a large reduction in root growth with clay (45-55%) but not with sandy loam soil (<20%). Treated wastewater increased salt uptake, membrane leakage and proline content, and decreased root viability, carbohydrate content and osmotic potentials in the fine roots, especially in clay. These results provide evidence that TWW challenges and damages the root system. The phenology and physiology of root orders were studied in lysimeters. Soil type influenced diameter, specific root area, tissue density and cortex area similarly in all root orders, while TWW influenced these only in clay soil. Respiration rates were similar in both soils, and root hydraulic conductivity was severely reduced in clay soil. Treated wastewater increased respiration rate and reduced hydraulic conductivity of all root orders in clay but only of the lower root orders in sandy loam soil. Loss of hydraulic conductivity increased with root order in clay and clay irrigated with TWW. Respiration and hydraulic properties of all root orders were significantly affected by sodium-amended TWW in sandy loam soil. These changes in root order morphology, anatomy, physiology and hydraulic properties indicate rapid and major modifications of root systems in response to differences in soil type and water quality. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Real time control and numerical simulation of pipeline subjected to landslide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cuscuna, S.; Giusti, G.; Gramola, C.

1984-06-01

This paper describes SNAM research activity in the study of behaviour and real-time control of pipelines in landslide areas. The subject can be delt considering three different aspects: 1. Geotechnical characterization of unstable soils. The mechanical parameters of soil and the landslide types are defined; 2. Structural analysis of pipe-soil system. By means of a finite element program it's possible to study the pipe-soil interaction; in this numerical code the soil parameters attend by the non-linear elastic behaviour of pipe restraints. The results of this analysis are the location of the expected most stressed sections of pipe and the globalmore » behaviour of pipe inside the soil. 3. Instrumental control. The adoption of a suitable appliance of vibrating wire strain gauges allows the strain control of pipe in time. The aim is to make possible timely interventions in order to guarantee the installation safety.« less

Is it efficient to co-compost and co-vermicompost green waste with biochar and/or clay to reduce CO2 emissions? A short-term laboratory experiment on (vermi)composts with additives.

NASA Astrophysics Data System (ADS)

Barthod, Justine; Rumpel, Cornélia; Paradelo, Remigio; Dignac, Marie-France

2016-04-01

Intensive farming practices can lead to a depletion of soil organic matter, negatively impacting important soil properties such as structural stability, fertility and C storage. The addition of organic amendments such as compost and vermicompost, rich in carbon, helps maintaining soil organic matter levels or restoring degraded soils. Composting and vermicomposting are based on stabilization of organic matter through the mineralization of easily decomposable organic matter compounds, therefore releasing greenhouse gases, including CO2. The aim of this study was to evaluate the global potential reduction of such emissions by the use of additives (2:1 clay and/or biochar): during (vermi)composting processes and after use of the final products as soil amendments. We hypothesized that the interactions between the additives and organic matter may lead to carbon stabilization and that such interactions may be enhanced by the presence of worms (Eisenia). We added in different proportions clay (25% or 50%), biochar (10%) and a mixture of biochar (10%) with clay (25%) to pre-composted green waste. The CO2 emissions of the composting and vermicomposting processes were measured during 21 days. After that, the amendments were added to a loamy cambisol soil and the CO2 emissions were monitored during 30 days of a laboratory experiment. The most efficient treatments in terms of reducing global CO2 emissions were the co-vermicomposting process with 25% clay followed by co-composting with 50% clay and with 10% biochar plus 25% clay. In this treatment (vermicompost with 25% clay), the carbon emissions were decreased by up to 44% compared to regular compost. Addition of biochar reduced CO2 emissions only during composting. Co-composting with biochar could be a promising avenue to limit global CO2 emissions whereas in presence of worms clay additions are better suited. These findings suggest that the presence of worms increased the formation of organo-mineral associations and thus C protection up to a certain clay/organic matter ratio. This strategy could be used to enhance the stability of organic amendments and increase soil carbon sequestration.

Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils.

PubMed

Meeboon, Naruemon; Leewis, Mary-Cathrine; Kaewsuwan, Sireewan; Maneerat, Suppasil; Leigh, Mary Beth

2017-08-01

Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.

The Preparation of Gelatine-Embedded Soil and Litter Sections and Their Application to Some Soil Ecological Studies.

ERIC Educational Resources Information Center

Anderson, J. M.

1978-01-01

A method is described for preparing large gelatine-embedded soil sections for ecological studies. Sampling methods reduce structural disturbance of the samples to a minimum and include freezing the samples in the field to kill soil invertebrates in their natural microhabitats. Projects are suggested for upper secondary school students. (Author/BB)

Enhancing Bioremediation of Oil-contaminated Soils by Controlling Nutrient Transport using Dual Characteristics of Soil Pore Structure

NASA Astrophysics Data System (ADS)

Mori, Y.; Suetsugu, A.; Matsumoto, Y.; Fujihara, A.; Suyama, K.; Miyamoto, T.

2012-12-01

Soil structure is heterogeneous with cracks or macropores allowing bypass flow, which may lead to applied chemicals avoiding interaction with soil particles or the contaminated area. We investigated the bioremediation efficiency of oil-contaminated soils by applying suction at the bottom of soil columns during bioremediation. Unsaturated flow conditions were investigated so as to avoid bypass flow and achieve sufficient dispersion of chemicals in the soil column. The boundary conditions at the bottom of the soil columns were 0 kPa and -3 kPa, and were applied to a volcanic ash soil with and without macropores. Unsaturated flow was achieved with -3 kPa and an injection rate of 1/10 of the saturated hydraulic conductivity. The resultant biological activities of the effluent increased dramatically in the unsaturated flow with macropores condition. Unsaturated conditions prevented bypass flow and allowed dispersion of the injected nutrients. Unsaturated flow achieved 60-80% of saturation, which enhanced biological activity in the soil column. Remediation results were better for unsaturated conditions because of higher biological activity. Moreover, unsaturated flow with macropores achieved uniform remediation efficiency from upper through lower positions in the column. Finally, taking the applied solution volume into consideration, unsaturated flow with -3 kPa achieved 10 times higher efficiency when compared with conventional saturated flow application. These results suggest that effective use of nutrients or remediation chemicals is possible by avoiding bypass flow and enhancing biological activity using relatively simple and inexpensive techniques.

Soil Microbial Community Responses to Long-Term Global Change Factors in a California Grassland

NASA Astrophysics Data System (ADS)

Qin, K.; Peay, K.

2015-12-01

Soil fungal and bacterial communities act as mediators of terrestrial carbon and nutrient cycling, and interact with the aboveground plant community as both pathogens and mutualists. However, these soil microbial communities are sensitive to changes in their environment. A better understanding of the response of soil microbial communities to global change may help to predict future soil microbial diversity, and assist in creating more comprehensive models of terrestrial carbon and nutrient cycles. This study examines the effects of four global change factors (increased temperature, increased variability in precipitation, nitrogen deposition, and CO2 enrichment) on soil microbial communities at the Jasper Ridge Global Change Experiment (JRGCE), a full-factorial global change manipulative experiment on three hectares of California grassland. While similar studies have examined the effects of global change on soil microbial communities, few have manipulated more factors or been longer in duration than the JRGCE, which began field treatments in 1998. We find that nitrogen deposition, CO2 enrichment, and increased variability in precipitation significantly affect the structure of both fungal and bacterial communities, and explain more of the variation in the community structures than do local soil chemistry or aboveground plant community. Fungal richness is correlated positively with soil nitrogen content and negatively with soil water content. Arbuscular mycorrhizal fungi (AMF), which associate closely with herbaceous plants' roots and assist in nutrient uptake, decrease in both richness and relative abundance in elevated CO2 treatments.

Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests.

PubMed

Waring, Bonnie G; Adams, Rachel; Branco, Sara; Powers, Jennifer S

2016-01-01

Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free-living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale-explicit sampling strategy to examine soil N cycling at scales ranging from the microsite to ecosystem level. We measured fungal community composition, total and inorganic N pools, gross proteolytic rate, net N mineralization and microbial extracellular enzyme activity at multiple locations within 18 permanent plots that span dramatic gradients of soil N concentration, stand age and forest composition. The ratio of inorganic to organic N cycling was correlated with variation in fungal community structure, consistent with a strong influence of ectomycorrhiza on ecosystem-scale N cycling. However, on average, > 61% of the variation in soil biogeochemistry occurred within plots, and the effects of forest composition were mediated by this local-scale heterogeneity in total soil N concentrations. These cross-scale interactions demonstrate the importance of a spatially explicit approach towards an understanding of controls on element cycling. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

PubMed Central

Liang, Yuting; Zhao, Huihui; Deng, Ye; Zhou, Jizhong; Li, Guanghe; Sun, Bo

2016-01-01

With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions. PMID:26870020

N2O and N2 emissions from contrasting soil environments - interactive effects of soil nitrogen, hydrology and microbial communities

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Elberling, Bo; Ribbons, Relena; Hedo, Javier; José Fernández Alonso, Maria; Krych, Lukasz; Sandris Nielsen, Dennis; Kitzler, Barbara

2016-04-01

Reactive nitrogen (N) in the environment has doubled relative to the natural global N cycle with consequences for biogeochemical cycling of soil N. Also, climate change is expected to alter precipitation patterns and increase soil temperatures which in Arctic environments may accelerate permafrost thawing. The combination of changes in the soil N cycle and hydrological regimes may alter microbial transformations of soil N with unknown impacts on N2O and N2 emissions from temperate and Arctic soils. We present the first results of soil N2O and N2 emissions, chemistry and microbial communities over soil hydrological gradients (upslope, intermediate and wet) across a global N deposition gradient. The global gradient covered an N-limited high Arctic tundra (Zackenberg-ZA), a pacific temperate rain forest (Vancouver Island-VI) and an N saturated forest in Austria (Klausenleopoldsdorf-KL). The N2O and N2 emissions were measured from intact cores at field moisture in a He-atmosphere system. Extractable NH4+ and NO3-, organic and microbial C and N and potential enzyme-activities were determined on soil samples. Soil genomic DNA was subjected to MiSeq-based tag-encoded 16S rRNA and ITS gene amplicon sequencing for the bacterial and fungal community structure. Similar soil moisture levels were observed for the upslope, intermediate and wet locations at ZA, VI and KL, respectively. Extractable NO3- was highest at the N rich KL and lowest at ZA and showed no trend with soil moisture similar to NH4+. At ZA and VI soil NH4+ was higher than NO3- indicating a tighter N cycling. N2O emissions increased with soil moisture at all sites. The N2O emissions for the wet locations ranked similarly to NO3- with the largest response to soil moisture at KL. N2 emissions were remarkably similar across the sites and increased with soil wetness. Microbial C and N also increased with soil moisture and were overall lowest at the N rich KL site. The potential activity of protease enzyme was site dependent indicating different capacities for N turnover of the microbial community. These findings indicate a positive feedback between increased soil N and wetter soils that promotes N2O relative to N2. These interactions may be site specific due to differential functional diversity of the soil microbial community. Future characterization of the community structure will shed light on the link between the role of microbial groups related to soil N cycling pathways and the resultant partitioning of N2O and N2 emissions in these contrasting environments.

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function.

PubMed

Gavazov, Konstantin; Ingrisch, Johannes; Hasibeder, Roland; Mills, Robert T E; Buttler, Alexandre; Gleixner, Gerd; Pumpanen, Jukka; Bahn, Michael

2017-07-15

Seasonal snow cover provides essential insulation for mountain ecosystems, but expected changes in precipitation patterns and snow cover duration due to global warming can influence the activity of soil microbial communities. In turn, these changes have the potential to create new dynamics of soil organic matter cycling. To assess the effects of experimental snow removal and advanced spring conditions on soil carbon (C) and nitrogen (N) dynamics, and on the biomass and structure of soil microbial communities, we performed an in situ study in a subalpine grassland in the Austrian Alps, in conjunction with soil incubations under controlled conditions. We found substantial winter C-mineralisation and high accumulation of inorganic and organic N in the topsoil, peaking at snowmelt. Soil microbial biomass doubled under the snow, paralleled by a fivefold increase in its C:N ratio, but no apparent change in its bacteria-dominated community structure. Snow removal led to a series of mild freeze-thaw cycles, which had minor effects on in situ soil CO 2 production and N mineralisation. Incubated soil under advanced spring conditions, however, revealed an impaired microbial metabolism shortly after snow removal, characterised by a limited capacity for C-mineralisation of both fresh plant-derived substrates and existing soil organic matter (SOM), leading to reduced priming effects. This effect was transient and the observed recovery in microbial respiration and SOM priming towards the end of the winter season indicated microbial resilience to short-lived freeze-thaw disturbance under field conditions. Bacteria showed a higher potential for uptake of plant-derived C substrates during this recovery phase. The observed temporary loss in microbial C-mineralisation capacity and the promotion of bacteria over fungi can likely impede winter SOM cycling in mountain grasslands under recurrent winter climate change events, with plausible implications for soil nutrient availability and plant-soil interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

Lasting effect of soil warming on organic matter decomposition depends on tillage practices

USDA-ARS?s Scientific Manuscript database

Global warming affects various parts of carbon (C) cycle including acceleration of soil organic matter (SOM) decomposition with strong feedback to atmospheric CO2 concentration. Despite many soil warming studies showed changes of microbial community structure, very few were focused on the effect of ...

Keeping your forest soils healthy and productive.

Treesearch

Ole T. Helgerson; Richard E. Miller

2008-01-01

Soils are an integral structural part of your woodland and the larger forest ecosystem. Important forest soil functions include:Providing water, nutrients, and physical support for the growth of trees and other forest plantsAllowing an exchange of carbon dioxide, oxygen, and other gasses that affect root growth and...

Effects of nano-SiO2 on the adsorption of chiral metalaxyl to agricultural soils.

PubMed

Huang, Junxing; Liang, Chuanzhou; Zhang, Xu

2017-06-01

The application of nanotechnology in agriculture, pesticide delivery and other related fields increases the occurrence of engineered nanoparticles (ENPs) in soil. Since ENPs have larger surface areas and normally a high adsorption capacity for organic pollutants, they are thought to influence the transport of pesticides in soils and thereafter influence the uptake and transformation of pesticides. The adsorption pattern of racemic-metalaxyl on agricultural soils including kinetics and isotherms changed in the presence of nano-SiO 2 . The adsorption of racemic-metalaxyl on agricultural soil was not enantioselective, in either the presence or the absence of SiO 2 . The adsorption of racemic-metalaxyl on SiO 2 decreased to some extent in soil-SiO 2 mixture, and the absolute decrease was dependent on soil properties. The decreased adsorption of metalaxyl on SiO 2 in soil-SiO 2 mixture arose from the competitive adsorption of soil-dissolved organic matter and the different dispersion and aggregation behaviors of SiO 2 in the presence of soil. Interactions between SiO 2 and soil particles also contributed to the decreased adsorption of metalaxyl on SiO 2 , and the interactions were analyzed by extended Derjaguin-Landau-Verwey-Overbeek theory. The results showed that the presence of nano-particles in soils could decrease the mobility of pesticides in soils and that this effect varied with different soil compositions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of Tire Tractive Performance on Deformable Terrain by Finite Element-Discrete Element Method

NASA Astrophysics Data System (ADS)

Nakashima, Hiroshi; Takatsu, Yuzuru

The goal of this study is to develop a practical and fast simulation tool for soil-tire interaction analysis, where finite element method (FEM) and discrete element method (DEM) are coupled together, and which can be realized on a desktop PC. We have extended our formerly proposed dynamic FE-DE method (FE-DEM) to include practical soil-tire system interaction, where not only the vertical sinkage of a tire, but also the travel of a driven tire was considered. Numerical simulation by FE-DEM is stable, and the relationships between variables, such as load-sinkage and sinkage-travel distance, and the gross tractive effort and running resistance characteristics, are obtained. Moreover, the simulation result is accurate enough to predict the maximum drawbar pull for a given tire, once the appropriate parameter values are provided. Therefore, the developed FE-DEM program can be applied with sufficient accuracy to interaction problems in soil-tire systems.

Influences and interactions of inundation, peat, and snow on active layer thickness: Modeling Archive

DOE Data Explorer

Scott Painter; Ethan Coon; Cathy Wilson; Dylan Harp; Adam Atchley

2016-04-21

This Modeling Archive is in support of an NGEE Arctic publication currently in review [4/2016]. The Advanced Terrestrial Simulator (ATS) was used to simulate thermal hydrological conditions across varied environmental conditions for an ensemble of 1D models of Arctic permafrost. The thickness of organic soil is varied from 2 to 40cm, snow depth is varied from approximately 0 to 1.2 meters, water table depth was varied from -51cm below the soil surface to 31 cm above the soil surface. A total of 15,960 ensemble members are included. Data produced includes the third and fourth simulation year: active layer thickness, time of deepest thaw depth, temperature of the unfrozen soil, and unfrozen liquid saturation, for each ensemble member. Input files used to run the ensemble are also included.

Derivation of thermokarst distribution based on climate and surface characteristics

NASA Astrophysics Data System (ADS)

Schöngaßner, Thomas; Hagemann, Stefan

2013-04-01

About one quarter of the northern hemisphere is covered by permafrost. Permafrost areas inherit a high amount of deposited soil organic carbon, which represents approximately 50% of the estimated global below-ground organic carbon pool and is more than twice the size of the current atmospheric carbon pool. A destabilization due to the expected amplitude of future Arctic climate warming would lead to a global-scale feedback mechanism. This feedback comprise interactions between snow, permafrost, hydrology, and ecosystems, which include altered energy and water fluxes between atmosphere and land surface. The representation of permafrost related processes in GCMs and ESMs is still rudimentary and needs to be extended to improve the climate model performance in high latitudes. In this sense thermokarst processes should be included into JSBACH, the land-surface component of MPI-ESM. Initially, a 1-D scheme of thermal dynamics will be implemented into JSBACH, which fits into very recent developments with regards to permafrost melting and freezing (T. Blome; Ekici et al., in prep.) and a dynamical wetland scheme (Stacke and Hagemann, 2012). Structural improvements and new parametrization of the model are required with regard to heat and water flow (physical processes) and carbon and nitrogen dynamics (bio-geochemical processes). The implementation of a thermokarst module is one task within the EU project PAGE21 and is a joint activity between MPI-M Hamburg and MPI-BGC Jena. Thermokarst changes are coupled thermal-hydrological processes, which lead to an enhanced thawing of ice-rich permafrost on local-to-regional scales, where the soil structure is characterized by segregated ice and ice-wedges. They result in severe consequences for soil structure, hydrology, and depletion of soil organic carbon. Thermokarst affected areas appear as a very uneven surface of hummocks and marshy hollows. The initial heat balance of the surface is disturbed by different trigger mechanisms, which cause the ground ice to melt and the soil to subside into depressions due to developing cavities in the interior. The depressions fill up with melting and precipitating water. Since deeper water bodies do not freeze up entirely, the annual mean surface temperature increases in the soil beneath. Therefore permafrost thawing is continued and depressions grow further due to soil subsidence and slope wash at the margins until a new soil surface heat balance is reached. Here I'd like to give a short overview and an introduction into the ongoing thermokarst process in the Arctic tundra. The main focus will be on investigating the actual distribution of thermokarst lakes in the high northern latitudes. The development of thermokarst lakes depends on soil parameters like ice content, surface temperature, soil texture as well as on climate states like monthly mean temperature, precipitation, winter snow depth. They contribute to the surface heat balance and may serve as a measure for thermokarst potential. Since thermokarst mechanism is a small-scale process of 10-1000m in spatial extent, it needs to be parametrized for GCM applications on ESM grid scale. Thus, we want to derive the thermokarst distribution as a function of climate and soil parameters.

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

PubMed

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents.

PubMed

Ochoa-Hueso, Raúl; Collins, Scott L; Delgado-Baquerizo, Manuel; Hamonts, Kelly; Pockman, William T; Sinsabaugh, Robert L; Smith, Melinda D; Knapp, Alan K; Power, Sally A

2018-03-05

The effects of short-term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought-induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant-microbial interactions and a greater incidence of certain soil-borne diseases. © 2018 John Wiley & Sons Ltd.

Coupling root architecture and pore network modeling - an attempt towards better understanding root-soil interactions

NASA Astrophysics Data System (ADS)

Leitner, Daniel; Bodner, Gernot; Raoof, Amir

2013-04-01

Understanding root-soil interactions is of high importance for environmental and agricultural management. Root uptake is an essential component in water and solute transport modeling. The amount of groundwater recharge and solute leaching significantly depends on the demand based plant extraction via its root system. Plant uptake however not only responds to the potential demand, but in most situations is limited by supply form the soil. The ability of the plant to access water and solutes in the soil is governed mainly by root distribution. Particularly under conditions of heterogeneous distribution of water and solutes in the soil, it is essential to capture the interaction between soil and roots. Root architecture models allow studying plant uptake from soil by describing growth and branching of root axes in the soil. Currently root architecture models are able to respond dynamically to water and nutrient distribution in the soil by directed growth (tropism), modified branching and enhanced exudation. The porous soil medium as rooting environment in these models is generally described by classical macroscopic water retention and sorption models, average over the pore scale. In our opinion this simplified description of the root growth medium implies several shortcomings for better understanding root-soil interactions: (i) It is well known that roots grow preferentially in preexisting pores, particularly in more rigid/dry soil. Thus the pore network contributes to the architectural form of the root system; (ii) roots themselves can influence the pore network by creating preferential flow paths (biopores) which are an essential element of structural porosity with strong impact on transport processes; (iii) plant uptake depend on both the spatial location of water/solutes in the pore network as well as the spatial distribution of roots. We therefore consider that for advancing our understanding in root-soil interactions, we need not only to extend our root models, but also improve the description of the rooting environment. Until now there have been no attempts to couple root architecture and pore network models. In our work we present a first attempt to join both types of models using the root architecture model of Leitner et al., (2010) and a pore network model presented by Raoof et al. (2010). The two main objectives of coupling both models are: (i) Representing the effect of root induced biopores on flow and transport processes: For this purpose a fixed root architecture created by the root model is superimposed as a secondary root induced pore network to the primary soil network, thus influencing the final pore topology in the network generation. (ii) Representing the influence of pre-existing pores on root branching: Using a given network of (rigid) pores, the root architecture model allocates its root axes into these preexisting pores as preferential growth paths with thereby shape the final root architecture. The main objective of our study is to reveal the potential of using a pore scale description of the plant growth medium for an improved representation of interaction processes at the interface of root and soil. References Raoof, A., Hassanizadeh, S.M. 2010. A New Method for Generating Pore-Network Models. Transp. Porous Med. 81, 391-407. Leitner, D, Klepsch, S., Bodner, G., Schnepf, S. 2010. A dynamic root system growth model based on L-Systems. Tropisms and coupling to nutrient uptake from soil. Plant Soil 332, 177-192.

Correlation of soil and sediment organic matter polarity to aqueous sorption of nonionic compounds

USGS Publications Warehouse

Kile, D.E.; Wershaw, R. L.; Chiou, C.T.

1999-01-01

Polarities of the soiL/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment sam pies were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (K(oc)) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxylamide-ester carbons. A plot of the measured partition coefficients (K(oc)) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of K(oc) values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in K(oc) between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with K(oc) illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.Polarities of the soil/sediment organic matter (SOM) in 19 soil and 9 freshwater sediment samples were determined from solid-state 13C-CP/MAS NMR spectra and compared with published partition coefficients (Koc) of carbon tetrachloride (CT) from aqueous solution. Nondestructive analysis of whole samples by solid-state NMR permits a direct assessment of the polarity of SOM that is not possible by elemental analysis. The percent of organic carbon associated with polar functional groups was estimated from the combined fraction of carbohydrate and carboxyl-amide-ester carbons. A plot of the measured partition coefficients (Koc) of carbon tetrachloride (CT) vs. percent polar organic carbon (POC) shows distinctly different populations of soils and sediments as well as a roughly inverse trend among the soil/sediment populations. Plots of Koc values for CT against other structural group carbon fractions did not yield distinct populations. The results indicate that the polarity of SOM is a significant factor in accounting for differences in Koc between the organic matter in soils and sediments. The alternate direct correlation of the sum of aliphatic and aromatic structural carbons with Koc illustrates the influence of nonpolar hydrocarbon on solute partition interaction. Additional elemental analysis data of selected samples further substantiate the effect of the organic matter polarity on the partition efficiency of nonpolar solutes. The separation between soil and sediment samples based on percent POC reflects definite differences of the properties of soil and sediment organic matters that are attributable to diagenesis.

Plants and microorganisms as drivers of mineral weathering

NASA Astrophysics Data System (ADS)

Dontsova, K.; Chorover, J.; Maier, R.; Hunt, E.; Zaharescu, D. G.

2011-12-01

Plants and microorganisms play important role in mineral weathering and soil formation modifying their environment to make it more hospitable for life. This presentation summarizes several collaborative studies that focused on understanding how interactions between plants and microorganisms, where plants provide the energy through photosynthesis, drive mineral weathering and result in soil formation. Plants influence weathering through multiple mechanisms that have been previously established, such as increase in CO2 concentration in the soil through root respiration and degradation of plant residues and exudates by heterotrophic microorganisms, release of organic acids that promote mineral dissolution, removal of weathering products from soil solution through uptake, and water redistribution. Weathering processes result in nutrient release that satisfies immediate needs of the plants and microorganisms, as well as precipitation of secondary phases, that provide surfaces for retention of nutrients and organic carbon accumulation. What makes understanding contribution of plants and microorganisms, such as bacteria and fungi, to mineral weathering challenging is the fact that they closely interact, enhancing and amplifying each other's contribution. In order to address multiple processes that contribute to and result from biological weathering a combination of chemical, biological, mineralogical, and computational techniques and methodologies is needed. This complex array of methodologies includes bulk techniques, such as determination of total dissolved organic and inorganic carbon and nitrogen, ion chromatography and high performance liquid chromatography to characterize amount and composition of exuded organic acids, inductively coupled plasma mass spectrometry to determine concentrations of lithogenic elements in solution, X-ray diffraction to characterize changes in mineral composition of the material, DNA extraction to characterize community structure, as well as microscopic techniques. These techniques in combination with numerical geochemical modeling are being employed to improve our understanding of biological weathering.

Interaction of polar and nonpolar organic pollutants with soil organic matter: sorption experiments and molecular dynamics simulation.

PubMed

Ahmed, Ashour A; Thiele-Bruhn, Sören; Aziz, Saadullah G; Hilal, Rifaat H; Elroby, Shaaban A; Al-Youbi, Abdulrahman O; Leinweber, Peter; Kühn, Oliver

2015-03-01

The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question "How organic pollutants interact with SOM?" is still lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model and carried out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), simulating the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and theoretical investigations explored four major points regarding sorption of SAA and HCB on soil, yielding the following results. 1--The interaction depends on the SOM chemical composition more than the SOM content. 2--The interaction causes a site-specific adsorption on the soil surfaces. 3--Sorption hysteresis occurs, which can be explained by inclusion of these pollutants inside soil voids. 4--The hydrophobic HCB is adsorbed on soil stronger than the hydrophilic SAA. Moreover, the theoretical results showed that HCB forms stable complexes with all SOM models in the aqueous solution, while most of SAA-SOM complexes are accompanied by dissociation into SAA and the free SOM models. The SOM-cavity modeling had a significant effect on binding of organic pollutants to SOM. Both HCB and SAA bind to the SOM models in the order of models with a small cavity>a large cavity>no cavity. Although HCB binds to all SOM models stronger than SAA, the latter is more affected by the presence of the cavity. Finally, HCB and SAA bind to the hydrophobic functional group (naphthalene) stronger than to the hydrophilic one (carboxylic acid) for all SOM models containing a cavity. For models without a cavity, SAA binds to carboxylic acid stronger than to naphthalene. Copyright © 2014 Elsevier B.V. All rights reserved.

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

PubMed Central

Skvortsova, Elena B.; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity. PMID:26010779

Universal spatial correlation functions for describing and reconstructing soil microstructure.

PubMed

Karsanina, Marina V; Gerke, Kirill M; Skvortsova, Elena B; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity.

Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Amity; Reardon, Patrick N.; Chacon, Stephany S.

Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na+-montmorillonite (001), Ca2+-montmorillonite (001), goethite (100), and Na+-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, four-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvatedmore » structure without these mineral surfaces present. Over the Na+-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.« less

Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure.

PubMed

Ishaq, Suzanne L; Johnson, Stephen P; Miller, Zach J; Lehnhoff, Erik A; Olivo, Sarah; Yeoman, Carl J; Menalled, Fabian D

2017-02-01

Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.

Impacts of Quaternary History on Critical Zone Structure and Processes: Examples and a Conceptual Model from the Intensively Managed Landscapes Critical Zone Observatory

NASA Astrophysics Data System (ADS)

Anders, Alison M.; Bettis, E. Arthur; Grimley, David A.; Stumpf, Andrew J.; Kumar, Praveen

2018-03-01

The concept of a critical zone (CZ) supporting terrestrial life has fostered groundbreaking interdisciplinary science addressing complex interactions among water, soil, rock, air and life near Earth’s surface. Pioneering work has focused on the CZ in areas with residual soils and steady-state or erosional topography. CZ evolution in these areas is conceptualized as progressive weathering of local bedrock (e.g. in the flow-through reactor model). However, this model is not applicable to areas in which weathering profiles form in transported materials including the formerly glaciated portion of the Central Lowland of North America. We present a new conceptual model of CZ evolution in landscapes impacted by continental glaciation based on investigations at three study sites in the Intensively Managed Landscapes Critical Zone Observatory (IML-CZO) The IML-CZO is devoted to the study of CZ processes in a region characterized by thick surficial deposits resulting from multiple continental glaciations, with bedrock at depths of up to 150 m. Here the physical (glacial ice, loess, developing soil profiles) and biological (microbes, tundra, forest, prairie) components of the CZ vary significantly in time. Moreover, the spatial relationships between mineral components of the CZ record a history of glacial-interglacial cycles and landscape evolution. We present cross-sections from IML-CZO sites to provide specific examples of how environmental change is recorded by the structure of the mineral components of the CZ. We build on these examples to create an idealized model of CZ evolution through a glacial cycle that represents the IML-CZO sites and other areas of low relief that have experienced continental glaciation. In addition, we identify two main characteristics of CZ structure which should be included in a conceptual model of CZ development in the IML-CZO and similar settings: (1) mineral components have diverse origins and transport trajectories including alteration in past CZs, and, (2) variability in climate, ecosystems, and hydrology during glacial-interglacial cycles profoundly influence the CZ composition, creating a legacy retained in its structure. This legacy is important because the current physical CZ structure influences the occurrence and rates of CZ processes, as well as future CZ responses to land use and climate change.

Contribution of species-specific chemical signatures to soil organic matter in Kohala, HI.

NASA Astrophysics Data System (ADS)

Stewart, C. E.; Amatangelo, K.; Neff, J. C.

2008-12-01

Soil organic matter (SOM) inherits much of its chemical structure from the dominant vegetation, including phenolic (lignin-derived), aromatic, and aliphatic (cutin and wax-derived) compounds. The Hawaiian fern species Dicranopteris decomposes more slowly than the angiosperm, Cheirodendron due to high concentrations of recalcitrant C compounds. These aliphatic fern leaf waxes are well-preserved and may comprise a large portion of the recalcitrant organic matter in these soils. Our objective was to determine the chemical signature of fern and angiosperm vegetation types and trace the preservation or loss of those compounds into the soil. We collected live tissue, litter, roots, and soil (<53 μm) from five dominant vegetation types including two angiosperms Cheirodendron and Metrosideros, two basal ferns Dicranopteris and Cibotium and a polypod fern Diplazium in Kohala, HI. We characterized them via TMAH-pyrolysis-gas chromatography-mass spectrometry. We found distinct chemical differences between angiosperm and fern vegetation; angiosperm contained more G- and S-derived lignin structures and the fern species contained greater relative abundances of P-derived lignin and tannin-derivatives. There was a general decrease of lignin-derived phenolic compounds from live to litter to soils and an increase in more recalcitrant, aromatic and aliphatic C. Recalcitrant fern-derived cutin and leaf waxes (alkene and alkanes structures) were evident in the soils, but clear species differences were not observed. Although ferns contain distinct lipid and wax-derived compounds, soils developed under fern do not appear to accumulate these compounds in SOM.

Pore-Water Carbonate and Phosphate As Predictors of Arsenate Toxicity in Soil.

PubMed

Lamb, Dane T; Kader, Mohammed; Wang, Liang; Choppala, Girish; Rahman, Mohammad Mahmudur; Megharaj, Mallavarapu; Naidu, Ravi

2016-12-06

Phytotoxicity of inorganic contaminants is influenced by the presence of competing ions at the site of uptake. In this study, interaction of soil pore-water constituents with arsenate toxicity was investigated in cucumber (Cucumis sativa L) using 10 contrasting soils. Arsenate phytotoxicity was shown to be related to soluble carbonate and phosphate. The data indicated that dissolved phosphate and carbonate had an antagonistic impact on arsenate toxicity to cucumber. To predict arsenate phytotoxicity in soils with a diverse range of soil solution properties, both carbonate and phosphate were required. The relationship between arsenic and pore-water toxicity parameters was established initially using multiple regression. In addition, based on the relationship with carbonate and phosphate we successively applied a terrestrial biotic ligand-like model (BLM) including carbonate and phosphate. Estimated effective concentrations from the BLM-like parametrization were strongly correlated to measured arsenate values in pore-water (R 2 = 0.76, P < 0.001). The data indicates that an ion interaction model similar to the BLM for arsenate is possible, potentially improving current risk assessments at arsenic and co-contaminated soils.

ECOUL: an interactive computer tool to study hydraulic behavior of swelling and rigid soils

NASA Astrophysics Data System (ADS)

Perrier, Edith; Garnier, Patricia; Leclerc, Christian

2002-11-01

ECOUL is an interactive, didactic software package which simulates vertical water flow in unsaturated soils. End-users are given an easily-used tool to predict the evolution of the soil water profile, with a large range of possible boundary conditions, through a classical numerical solution scheme for the Richards equation. Soils must be characterized by water retention curves and hydraulic conductivity curves, the form of which can be chosen among different analytical expressions from the literature. When the parameters are unknown, an inverse method is provided to estimate them from available experimental flow data. A significant original feature of the software is to include recent algorithms extending the water flow model to deal with deforming porous media: widespread swelling soils, the volume of which varies as a function of water content, must be described by a third hydraulic characteristic property, the deformation curve. Again, estimation of the parameters by means of inverse procedures and visualization facilities enable exploration, understanding and then prediction of soil hydraulic behavior under various experimental conditions.

Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

PubMed

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.

Soil Mineral Composition Matters: Response of Microbial Communities to Phenanthrene and Plant Litter Addition in Long-Term Matured Artificial Soils

PubMed Central

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications. PMID:25222697

Load and resistance factor design of bridge foundations accounting for pile group-soil interaction.

DOT National Transportation Integrated Search

2015-11-01

Pile group foundations are used in most foundation solutions for transportation structures. Rigorous and reliable pile design methods are : required to produce designs whose level of safety (probability of failure) is known. By utilizing recently dev...