Progress 09/01/08 to 08/31/10
Outputs
OUTPUTS: Without better understanding of the mechanisms associated with E. coli transport and survival in soil, the ability to minimize E. coli contamination of surface and ground waters will be limited. Soil matrix is a complex heterogeneous substrate with a wide range of variations in environmental settings existing at micro scales. These variations generate tremendous habitat diversity for soil microorganisms and affect their transport and survival. Last decade advances in X-ray computed microtomography allow obtaining 3-dimentional images of soil interiors with resolutions of just a few microns. The goal of this project was to study the relationship between pore distributions and structures within soil aggregates assessed using computed microtomography and E. coli distribution and transport in soils under different agricultural management practices. The project looked at the aggregates from the same soil type but under long-term (>18 years) differential land use and management settings at the NSF-funded Long Term Ecological Research experiment at Kellogg Biological Station. The land management practices that were considered are 1) conventionally plowed row crop agriculture; 2) conservationally managed (no-till) row crop agriculture ; and 3) native vegetation on land with previous agricultural use (native succession). The results indicate that long term differences in soil disturbance and management did result in substantially different intra-aggregate pore structures. The pore structure differences in-turn affected the ability of E.coli to enter soil macro-aggregates and to be retained within the aggregates during water flow events. The highest potential for the E.coli to be evenly distributed and retained within soil aggregates was observed for soil under conventionally plowed agricultural management, followed by no-till, and native succession aggregates. The highest potential for the E.coli to leave the aggregates during flow events was observed for native succession aggregates followed by no-till and conventionally plowed agricultural management. A total of 12 presentations at national and international conferences have been conducted during the course of the project. In addition to the 8 presentations of the preliminary results in 2009, in 2010 the results were reported at 4 national and international meetings (Soil Science Society of America, Joint Assembly of America Geophysical Union, World Congress of Soil Science, and Workshop on 3D Image Analysis). We expect 7 peer-review manuscripts as a result of the project. One of them has been published in 2009, two are in press, one is submitted, and three are in preparation. PARTICIPANTS: Project co-PIs are A.N.Kravchenko, J. Rose, and A. Smucker. The project allowed providing training opportunities for several undergraduate students; one Master student (Mr. Mustafa Mazer who worked on the project full time); four PhD students (Mr. Wei Wang and Ms. Katerina Ananyeva, who worked on the project full time and Mr. Tim Johnson and Dr. Sangeetha Srinivasan, who participated part time in project activities); and one post-doctoral research associate (Dr. Hyen Chun Chung). TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Project's stakeholders and products: Project's stakeholders are the environment research community interested in micro-scale microbial fate and transport in soils. Two new methods for processing intact soil aggregates have been developed in the course of the project. First, we devised a set of techniques for cutting intact soil aggregates into geo-referenced slices and relating the experimental measurements conducted on the slices with the micro-tomography image information. Second, a methodology has been developed and tested for conducting water flow, solute transport, and microbial transport experiments through the soil aggregates from coarse-textured soils with low aggregate stability. The proposed methods will be of interest to the soil, environment, and microbiology researchers working with intact soil samples and X-ray soil imaging. New knowledge generated: We found that 18-20 years of contrasting management led to substantial differences in pore structures of soil aggregates. Aggregates from native succession native vegetation and no-till agricultural management had more large connected pores located preferentially in the aggregate centers, while homogeneously spread medium-sized pores prevailed in conventionally-tilled soil aggregates. These differences manifested themselves in a greater flux of chemical solutes and E.coli through the native succession aggregates, while E.coli retention was greater in the conventionally-tilled aggregates. The entire aggregates were easily accessible to E.coli in conventionally-tilled soil, while aggregate centers were less accessible in no-till and native succession aggregates. Pore structures played an important role in E.coli redistribution within the aggregates and in E. coli potential for reentering the water current during a water flow event.
Publications
- Kravchenko A.N., Wang, W., H.C. Chun, M. Mazher A.J.M. Smucker, J.B. Rose, M.L. Rivers. 2011. Long-term land use affects aggregate porosity and E.coli redistribution within soil macro-aggregates Soil Sci. Soc. Am. J. (in preparation).
- Journal articles (submitted or in press): Smucker, A.J.M., W. Wang, A.N. Kravchenko and W.A. Dick. 2010. Forms and Functions of Meso and Micro-niches for Carbon within Soil Aggregates. Journal of Nematology Vol. 42 (in press).
- Kravchenko, A.N., R. E. Falconer, D. Grinev, W. Otten. 2010. Fungal colonization in soils of contrasting managements: modeling growth in 3D pore volumes of undisturbed soil samples. Ecological Applications (in press).
- Wang, W., A.N. Kravchenko, A.J.M. Smucker, and M.L. Rivers. 2010. A simulation study of image segmentation methods in microtomographic images of soil aggregates. Computers and Geoscience (submitted).
- Journal articles (in preparation): Wang, W., A.N. Kravchenko, A.J.M. Smucker, and M.L. Rivers. 2011. Intra-aggregate pore characteristics: X-ray computed microtomography analysis. Soil Sci. Soc. Am. J. (in preparation).
- Wang, W., T. Johnson, S. Srinivasan, A.J.M. Smucker, J.B. Rose, M.L. Rivers, and A.N. Kravchenko, 2011. E.coli redistribution and transport in intact soil macro-aggregates. Soil Sci. Soc. Am. J. (in preparation).
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Progress 09/01/08 to 08/31/09
Outputs
OUTPUTS: Major activities for each of the project Objectives: Objective 1: We have collected soil aggregate samples from three treatments: conventionally tilled and no-till agricultural managements and 20-year old native succession, from the Long Term Ecological Research site located at Kellogg Biological Station, Michigan. The aggregates were scanned at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), IL. X-rayed microtomographic 3D images were obtained for 20-30 aggregates of each treatment. The images were preprocessed and segmented into pore/solid space. Pore reconstructions using 3DMA-Rock software and modeling of the water/air fluxes in the 3D aggregate images using Lattice-Boltzmann approach are in progress. Objective 2: Because of low water stability of the studied coarse-textured aggregates, the originally proposed flow chambers for assessing E.coli movement proved to be unusable. Thus, we have developed a new glass bead matrix chamber system to saturate and perform solute and E.coli flow experiments through unstable aggregates. The flow through the chambers with/without soil aggregates has been tested using chloride solutions. Then, we determined optimal E.coli experimental conditions in terms of temperature, measurement times, E.coli concentrations, and E.coli application and measurement techniques. Methodology for analyses of the relationships between 3D pore structure and E.coli distribution within CT-scanned aggregates has been developed and the measurements and analyses are currently in progress. Objective 3: Several advanced statistical and modeling techniques have been explored for relating E.coli transport with 3D pore distributions, including, but not limited to geostatistical analyses, fractal and multifractal methods. Products: A methodology has been developed and tested for conducting water flow, solute transport, and microbial transport experiments through the soil aggregates from coarse-textured soils with low aggregate stability. A technical note is prepared for publication reporting the developed technique. We found that substantial differences have been formed in pore structures of soil aggregates during 18-20 years of contrasting management. Aggregates under native succession had overall lower porosity than aggregates from conventional tillage agriculture, while the percent of large connected pores in native succession aggregates was larger than in the conventionally tilled soil aggregates. The differences in pore space manifested themselves in greater flux of chemical solutes and E.coli through the native succession aggregates, while E.coli retention was greater in the conventionally tilled aggregates. Two manuscripts are currently in preparation reporting these results. A manuscript has been published on potential for multifractal methods for characterizing soil aggregate pore-size distributions. Events: Preliminary results have been reported in eight presentations (Annual Meeting of Soil Science Society of America, Joint Assembly of America Geophysical Union, and American Society for Microbiology General Meeting). PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
By looking with computer microtomography tools at a soil aggregate as a key building block of soil matrix, we can answer a number of questions clarifying fate and transport of pathogens in soil. As of now, it is clear that ability of E.coli to be retained within the soil matrix will differ not only among different soil types, but also within the same soil subjected to different land use and management. Soil pore structure does affect the ability of E. coli to be retained by soil aggregates, with conventionally tilled agriculture aggregates with larger numbers of small pores being able to retain greater numbers of E.coli than native succession aggregates with greater number of large well connected pores. The next step on which we are working at present is to determine what happens with E.coli once it is within the aggregate. Which parts of the aggregate it can reach in the aggregates with different pore structures, and what are the environmental conditions within the aggregate for it survival and regrowth Later, when the aggregate is subjected to saturated water flow during rainfall and runoff events, what are the E. coli numbers from within the aggregate that can leave the aggregate and become a potential surface water and groundwater contaminant
Publications
- Journal articles: Kravchenko A.N., Martin, M. A., Smucker, A., and Rivers, M. L. 2009. Theoretical and practical limitations in the determination of multifractal spectra from pore/solid soil aggregate images. Vadose Zone J., 8: 220-226.
- Abstracts: Smucker A.J.M., Chun, H. C., Ananyeva, K., Wang, W., Kravchenko, A., and Rose, J. 2009. Noninvasive Quantification of Intra-Aggregate Pore Geometries and Convective-Dispersive Flux of E. Coli, Ions and Carbon within Whole Soil Aggregates (abstract). Annual Meeting of Soil Science Society of America, Nov 3-5, Pittsburgh, PA.
- Ananyeva, K., Wang, W., Smucker, A. J. M., Kravchenko A. N., and Rivers, M. L. 2009. Characterization of Porosity Gradient within the Soil Aggregates Using X-Ray Microtomography. (abstract). Annual Meeting of Soil Science Society of America, Nov 3-5, Pittsburgh, PA.
- Ananyeva, K., Wang, W., Smucker, A. J. M., Kravchenko, A. N., and Rivers, M. L. 2009. Comparison of Three Approaches to Measuring Individual Soil Aggregate Density. (abstract). Annual Meeting of Soil Science Society of America, Nov 3-5, Pittsburgh, PA.
- Smucker A.J.M., Mazher, M., Sul, W. J., Chun, H. C., Kravchenko, A., Rose, J., and Tartakovsky, A. M. 2009. Soil Aggregate Pores Controlling Water Flux Rates and Retentions of Microbes and Ions. (abstract). Annual Meeting of Soil Science Society of America, Nov 3-5, Pittsburgh, PA.
- Wang, W., Kravchenko, A. N., Ananyeva, K., Smucker, A. J. M., Lim, C.Y., and Rivers, M. L. 2009. A Simulation Study of Segmentation Methods On the Soil Aggregate Microtomographic Images. (abstract). Annual Meeting of Soil Science Society of America, Nov 3-5, Pittsburgh, PA.
- Wang, W., Kravchenko, A. N., Ananyeva, K., Smucker, A. J. M., Chun, H. C., and Rivers, M. L. 2009. Comparison of Intra-Aggregate Pore Characteristics From Soil in Conventional Row-Crop Agriculture and Native Succession Vegetation. (abstract). Annual Meeting of Soil Science Society of America, Nov 3-5, Pittsburgh, PA.
- Wang, W., Kravchenko, A. N., Ananyeva, K., Smucker, A. J.M., Lim, C. Y., and Rivers, M. L. 2009. A simulation study on segmentation methods of the soil aggregate microtomographic images. Joint Assembly of America Geophysical Union, May 24-27, Toronto, Canada.
- Mazher, M., Kravchenko, A., Smucker, A., and Rose, J. B. 2009. Detection of E. coli in Whole and Concentric Layers of Aggregates. 109th American Society for Microbiology General Meeting, May 17-21, Philadelphia, PA, USA.
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