Name: design and construction of an urban runoff research facility
Uploaded: 2014-08-08T13:00:00
Description: Watch this Scientific Journal Video about Design and Construction of an Urban Runoff Research Facility at JoVE.com

The authors gratefully acknowledge financial support from The Scotts Miracle-Gro Company for this facility. We are also appreciative to the Toro Co. for assistance with providing the irrigation controller. The vision and planning by the late Dr. Chris Steigler in the early stages of this project is also gratefully acknowledged. The authors would also like to thank Ms. N. Stanley for her technical assistance with sample preparation and analysis.

1. Site Selection
<ol>
	<li>Locate a suitably-sized area of undisturbed soil having a uniform 3-4% slope.</li>
	<li>Conduct a topographic survey and delineate an area approximately 10 m x&#160;100 m having an average 3.7&#177;0.5% slope.</li>
	<li>Divide the 10 m x&#160;100 m area into three blocks, each approximately 10 m x&#160;33.3 m (Figure 1).</li>
	<li>Subdivide each block into 8 field plots, each 4.1 m wide by 8.2 m long.</li>
	<li>Identify and document the soil series present in the study area....

<ol>
	<li>Fulton, W., Pendall, R., Nguyen, M., Harrison, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Who+sprawls+most?+How+growth+patterns+differ+across+the+U.S.+The+Brookings+Institution+Survey+Series.">Who sprawls most? How growth patterns differ across the U.S. The Brookings Institution Survey Series.</a> http://www.brookings.edu/~/media/research/files/reports/2001/7/metropolitanpolicy%20fulton/fulton. , (2001).</li><li>White, R. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+much+water+is+'enough'?+Using+PET+to+develop+water+budgets+for+residential+landscapes.">How much water is 'enough'? Using PET to develop water budgets for residential landscapes.</a> Proc. Texas Sec. Amer. Water Works Assoc. 7, 7 (2004).</li><li>Walsh, C. J., Roy, A. H., Feminella, J. W., Cottingham, P. D., Groffman, P. M., Morgan, R. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+urban+stream+syndrome:+current+knowledge+and+the+search+for+a+cure.">The urban stream syndrome: current knowledge and the search for a cure.</a> J. North Am. Benthol. Soc. 24, 706-723 (2005).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=4R+Plant+Nutrition:+A+Manual+for+Improving+the+Management+of+Plant+Nutrition.">4R Plant Nutrition: A Manual for Improving the Management of Plant Nutrition.</a> International Plant Nutrition Institute. , (2012).</li><li>Miyomoto, S., Chacon, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soil+salinity+of+urban+turf+area+irrigated+with+saline+water+II.+Soil+factors.">Soil salinity of urban turf area irrigated with saline water II. Soil factors.</a> Landsc. Urban Plan. 77, 28-38 (2006).</li><li>Steele, M. K., Aitkenhead-Peterson, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Urban+soils+of+Texas:+Relating+irrigation+sodicity+to+water-extractable+carbon+and+nutrients.">Urban soils of Texas: Relating irrigation sodicity to water-extractable carbon and nutrients.</a> Soil Sci. Soc. Am. J. 76, 972-982 (2012).</li><li>Steele, M. K., Aitkenhead-Peterson, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Salt+impacts+on+organic+carbon+and+nitrogen+leaching+from+senesced+vegetation.">Salt impacts on organic carbon and nitrogen leaching from senesced vegetation.</a> Biogeochem. 112, 245-259 (2013).</li><li>Washbusch, R. J., Selbig, W. R., Bannerman, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sources+of+phosphorus+in+stormwater+and+street+dirt+from+two+urban+residential+basins.">Sources of phosphorus in stormwater and street dirt from two urban residential basins.</a> National Conference on Tools for Urban Water Resource Management and Protection Proceedings. , (2000).</li><li>Pitt, R., Chen, S., Clark, S. E., Swenson, J., Ong, C. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compaction's+impacts+on+urban+storm-water+infiltration.">Compaction's impacts on urban storm-water infiltration.</a> J. Irrigation Drainage Eng. 134, 652-658 (2008).</li><li>Kelling, K. A., Peterson, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Urban+lawn+infiltration+rates+and+fertilizer+runoff+losses+under+simulated+rainfall.">Urban lawn infiltration rates and fertilizer runoff losses under simulated rainfall.</a> Soil Sci. Soc. Am. J. 39, 349-352 (1975).</li><li>Edmondson, J. L., Davies, Z. G., McCormack, S. A., Gaston, K. J., Leake, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Are+soils+in+urban+ecosystems+compacted?+A+citywide+analysis.">Are soils in urban ecosystems compacted? A citywide analysis.</a> Biol. Lett. 7, 771-774 (2011).</li><li>Cunningham, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+suburban+stream+syndrome:+Evaluating+land+use+and+stream+impairments+in+the+suburbs.">The suburban stream syndrome: Evaluating land use and stream impairments in the suburbs.</a> Phys. Geogr. 30, 269-284 (2009).</li><li>Erickson, J. E., Cisar, J. L., Volin, J. C., Snyder, G. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparing+nitrogen+runoff+and+leaching+between+newly+established+St.+Augustinegrass+turf+and+an+alternative+residential+landscape.">Comparing nitrogen runoff and leaching between newly established St. Augustinegrass turf and an alternative residential landscape.</a> Crop Sci. 41, 1889-1895 (2001).</li><li>Morton, T. G., Gold, A. J., Sullivan, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+overwatering+and+fertilization+on+nitrogen+losses+from+home+lawns.">Influence of overwatering and fertilization on nitrogen losses from home lawns.</a> J. Environ. Qual. 17, 124-130 (1988).</li><li>O'Dell, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Method+415.1+Organic+carbon,+total+(combustion+or+oxidation).">Method 415.1 Organic carbon, total (combustion or oxidation).</a> Methods for Chemical Analysis of Water and Wastes. , 415.1-415.3 (1983).</li><li>O'Dell, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+phosphorus+by+semi+automated+colorimetry.+Environmental+monitoring+systems+laboratory,+Office+of+research+and+development.">Determination of phosphorus by semi automated colorimetry. Environmental monitoring systems laboratory, Office of research and development.</a> U.S. Environmental Protection Agency. , (1993).</li><li>O'Dell, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+nitrate+nitrogen+by+semi+automated+colorimetry.+Revision+2.0+Edited+by+JW+O'Dell,+Environmental+monitoring+systems+laboratory.">Determination of nitrate nitrogen by semi automated colorimetry. Revision 2.0 Edited by JW O'Dell, Environmental monitoring systems laboratory.</a> Office of research and development, U.S. Environmental Protection Agency. , (1993).</li><li>O'Dell, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+ammonia+nitrogen+by+semi+automated+colorimetry.+Revision+2.0+Edited+by+JW+O'Dell,+Environmental+monitoring+systems+laboratory.">Determination of ammonia nitrogen by semi automated colorimetry. Revision 2.0 Edited by JW O'Dell, Environmental monitoring systems laboratory.</a> Office of research and development, U.S. Environmental Protection Agency. , (1993).</li><li>Gobel, P., Dierkes, C., Coldewey, W. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Storm+water+runoff+concentration+matrix+for+urban+areas.">Storm water runoff concentration matrix for urban areas.</a> J. Contam. Hydrol. 91, 26-42 (2007).</li><li>Vietor, D. M., Provin, T. L., White, R. H., Munster, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Runoff+losses+of+phosphorus+and+nitrogen+imported+in+sod+or+composted+manure+for+turf+establishment.">Runoff losses of phosphorus and nitrogen imported in sod or composted manure for turf establishment.</a> J. Env. Qual. 33, 358-366 (2004).</li></ol>

Water flow over, into, and through soils is greatly affected by the topography, vegetative cover, and the soil physical properties. Excessively compacted soils and soils with high clay contents will exhibit reduced infiltration rates and increased amounts of runoff. Therefore, when building a facility of this nature, every effort should be made to use native soils with uniform slopes and minimize compaction from all types of traffic on the experimental areas during construction. In addition, compaction from post construc...

Four of the most rapidly growing, highly populated metropolitan areas are located in the southern U.S. in subtropical climates1. In addition, the largest percent change in urbanized land between 1982 and 1997 occurred in southern USA1. With increased urban areas comes a concomitant demand for potable water,&#160;much of which is used for outdoor use during summer months2. With new construction, programmable in-ground irrigation systems are often installed. Unfortunately, these systems are often programmed to deliver irrigation to urban landscaping more frequently and/or in volumes that exceed evapotranspiration demands of the landscape2. This results in a significant volume of runoff from urban landscaping to receiving waters, which contributes to what has been termed urban stream syndrome3. Symptoms of the urban stream syndrome include increased frequency of overland flow and erosive flow, increased nitrogen (N), phosphorus (P), toxicants, and temperature in addition to changes in channel morphology, freshwater biology, and ecosystem processes3.
Losses of N and P from agricultural ecosystems have been extensively studied and found to be primarily dependent on four factors: nutrient source, application rate, application timing, and nutrient placement4. While fewer published data currently exist on off site movement of nutrients from urban landscapes, these principals can be directly applied to turfgrass culture, whether in home lawns, sod farms, parks, or other green spaces. Additionally, improper irrigation practices which result in runoff from the landscape can exacerbate these losses.
Nutrient losses can be further altered by irrigation water quality. Areas in the southwest US often utilize more saline or sodic water for irrigation of home lawns and urban landscapes5,6. The chemical composition of the irrigation water may significantly alter soil chemistry causing a release of carbon, nitrogen, calcium, and other cations to runoff water. Recent work showed that increased sodium absorption ratio (SAR) of the extracting water significantly increased the amounts of carbon (C) and nitrogen (N) leached from St. Augustinegrass clippings, ryegrass clippings, and other organic materials7. Furthermore, water extractable soil C, N, and P losses from recreational turfgrass soils were significantly correlated with irrigation water chemical constituents6.
Washbusch et al. studied urban runoff in Madison, WI and found that lawns were the largest contributors of total phosphorus8. In addition, they also found that 25% of the total P in &#8220;Street Dirt&#8221; originated from leaves and grass clippings. In a typical rural setting, leaf litter falls onto the ground and then decomposes slowly releasing nutrients back to the soil environment. However, in urban environments, significant quantities of nutrient-rich leaves and grass clippings may fall on or get washed or blown onto hardscapes such as driveways, sidewalks, and roadways, subsequently making their way into the streets where they contribute to &#8220;street dirt&#8221;, much of which gets washed directly into receiving waterways.
Urban landscape soils are often disturbed and highly compacted during construction, which can also increase amounts of runoff due to reduced infiltration rates9. Kelling and Peterson reported that both total runoff volume and the nutrient concentrations in runoff from home lawns are increased from lawns that are compacted or have severely disturbed soil profiles due to previous construction activities10. Edmondson et al. on the other hand, found that urban soils were less compacted compared to surrounding agricultural soils in the urban and suburban region of Leicester, UK11. They attributed this to heavy agricultural machinery used, but they also noted that lawns had a greater soil bulk density than soil under trees and shrubs which was attributed to grass mowing and greater human trampling.
It would appear that in many situations, urban and suburban stream syndromes are significantly impacted by runoff and point-source discharges3,12. While point-sources can be manipulated through permits and recycling, additional research is needed to develop and test best management procedures for home lawn establishment and management to minimize nutrient losses to runoff. Past research efforts in this regard have often been centered along coastal areas where there are high sand content soils, due to concerns related to the effects of leaching and runoff losses of nutrients to coastal waters. However, when working with very sandy soils, one must have steep slopes and high rainfall rates to be able to generate any runoff13,14. In contrast, many of the soils in the central United States are fine textured and have low infiltration rates that result in significant amounts of runoff from even small rainfall events. Thus, it was desired to design and construct a runoff facility on native soil and slope typical of those that may occur on residential landscapes.
This paper describes the design, construction and function of a 1,000 m2 facility containing 24 individual 33.6 m2 field plots for measuring total runoff volumes at relatively small temporal resolutions and simultaneous collection of runoff water subsamples at selected volumetric or temporal intervals for measurement and quantification of chemical constituents of the runoff water.

<table border="0" cellpadding="0" cellspacing="0" width="778">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:244px;">Flow meter</td>
			<td style="width:151px;">Teledyne Isco</td>
			<td style="width:216px;">Model 4230</td>
			<td style="width:167px;">Bubbling flow meter that measures and records water flow through flume</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Portable Sampler</td>
			<td>Teledyne Isco</td>
			<td>Model 6712</td>
			<td>Works in conjunction with the flow meter to collect water samples at predetermined intervals.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Flow Link Software to collect data</td>
			<td>Teledyne Isco</td>
			<td>Ver 5.0</td>
			<td>Allows communication between flow meter and computer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pre-sloped trench drain</td>
			<td>Zurn Industries, LLC</td>
			<td>Z-886</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Irrigation Controller</td>
			<td>Toro Company</td>
			<td>VP Satellite</td>
			<td>Controls irrigation to each plot individually</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Electric Valves</td>
			<td>Hunter</td>
			<td>2.5 cm PGV</td>
			<td>Opens or closes water flow to individual plots based on signal from irrigation controller</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Spray nozzles</td>
			<td>RainBird</td>
			<td>HE-Van 12</td>
			<td>Sprays irrigation water in predetermined pattern and rate</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Irrigation heads</td>
			<td>Hunter</td>
			<td>Pro Spray 4</td>
			<td>4 inch pop up spray heads</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">6 inch slotted drain pipe</td>
			<td>Advanced Drainage Systems</td>
			<td>6410100</td>
			<td>single wall corregated HDPE - slotted</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">6 inch plain drain pipe</td>
			<td>Advanced Drainage Systems</td>
			<td>6400100</td>
			<td>single wall corregated HDPE - plain</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Filter Paper</td>
			<td>Whatman GF/F</td>
			<td>1825-047</td>
			<td>47mm diameter, binder-free, glass microfiber filter</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pH Meter</td>
			<td>Fisher</td>
			<td>Accumet XL20</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Combination pH probe</td>
			<td>Fisher</td>
			<td>13-620-130</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Automatic Temperature Compensating Probe</td>
			<td>Fisher</td>
			<td>13-602-19</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Electrical conductivity probe</td>
			<td>Fisher</td>
			<td>13-620-100</td>
			<td>Cell constant of 1.0</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">&#160;TOC-VCSH with total nitrogen unit TMN-1</td>
			<td>Shimadzu Corp</td>
			<td>TOC-VCSH with TMN-1</td>
			<td>dissolved C and N analyzer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Smartchem 200</td>
			<td>Unity Scientific</td>
			<td>200</td>
			<td>Discrete Analyzer for P measurement</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">ICS 1000</td>
			<td>Dionex</td>
			<td>ICS 1000</td>
			<td>Ion Chromatography for Ca, Mg, K and Na measurment</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:244px;">Portable Soil Moisture Meter</td>
			<td>Spectrum&#160;</td>
			<td style="width:216px;">FieldScout TDR 300</td>
			<td>7.5 cm long probes</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:244px;">Totallizing Water Meters</td>
			<td style="width:151px;">Badger</td>
			<td style="width:216px;">3/4 inch water meters</td>
			<td>standard homeowner water meters</td>
		</tr>
	</tbody>
</table>

design and construction of an urban runoff research facility

As the urban population increases, so does the area of irrigated urban landscape. Summer water use in urban areas can be 2-3x winter base line water use due to increased demand for landscape irrigation. Improper irrigation practices and large rainfall events can result in runoff from urban landscapes which has potential to carry nutrients and sediments into local streams and lakes where they may contribute to eutrophication. A 1,000 m2 facility was constructed which consists of 24 individual 33.6 m2 field plots, each equipped for measuring total runoff volumes with time and collection of runoff subsamples at selected intervals for quantification of chemical constituents in the runoff water from simulated urban landscapes. Runoff volumes from the first and second trials had coefficient of variability (CV) values of 38.2 and 28.7%, respectively. CV values for runoff pH, EC, and Na concentration for both trials were all under 10%. Concentrations of DOC, TDN, DON, PO4-P, K+, Mg2+, and Ca2+ had CV values less than 50% in both trials. Overall, the results of testing performed after sod installation at the facility indicated good uniformity between plots for runoff volumes and chemical constituents. The large plot size is sufficient to include much of the natural variability and therefore provides better simulation of urban landscape ecosystems.

Plot characteristics 
The average slope for all 24 plots was 3.7% and ranged from a low of 3.2% for plot 17 to a high of 4.1% for plot 2 (Table 1). Average topsoil thickness was 36 cm and ranged from a low of 25.0 cm for plot 24 to a high of 51.5 cm for plot 10 (Table 1).
Runoff volumes 
Runoff volumes from the first trial on 09&#160;August 2012 had a mean of 213.5 L and ranged from a low of 95.6 L to a high of 391 L with a coefficient of variability...

Watch this Scientific Journal Video about Design and Construction of an Urban Runoff Research Facility at JoVE.com

Design and Construction of an Urban Runoff Research Facility

This paper describes the design, construction, and function of a 1,000 m2 facility containing 24 individual 33.6 m2 field plots equipped for measuring total runoff volumes with time and collection of runoff subsamples at selected intervals for quantification of chemical constituents in the runoff water from simulated home lawns.

As the urban population increases, so does the area of irrigated urban landscape. Summer water use in urban areas can be 2-3x winter base line water use ...

design-and-construction-of-an-urban-runoff-research-facility

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Environment

Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes and soil organic matter formation to small-scale stable-isotope biomarker probing. Coupling multiple stable isotopes such as 13C with 15N, 18O or&#160;2H has the potential to reveal even more information about complex stoichiometric relationships during biogeochemical transformations. Isotope labeled plant material has been used in various studies of litter decomposition and soil organic matter formation1-4. From these and other studies, however, it has become apparent that structural components of plant material behave differently than metabolic components (i.e. leachable low molecular weight compounds) in terms of microbial utilization and long-term carbon storage5-7. The ability to study structural and metabolic components separately provides a powerful new tool for advancing the forefront of ecosystem biogeochemical studies. Here we describe a method for producing 13C and 15N labeled plant material that is either uniformly labeled throughout the plant or differentially labeled in structural and metabolic plant components.
Here, we present the construction and operation of a continuous 13C and 15N labeling chamber that can be modified to meet various research needs. Uniformly labeled plant material is produced by continuous labeling from seedling to harvest, while differential labeling is achieved by removing the growing plants from the chamber weeks prior to harvest. Representative results from growing Andropogon gerardii Kaw demonstrate the system&#39;s ability to efficiently label plant material at the targeted levels. Through this method we have produced plant material with a 4.4 atom%13C and 6.7 atom%15N uniform plant label, or material that is differentially labeled by up to 1.29 atom%13C and 0.56 atom%15N in its metabolic and structural components (hot water extractable and hot water residual components, respectively). Challenges lie in maintaining proper temperature, humidity, CO2 concentration,&#160;and light levels in an airtight 13C-CO2 atmosphere for successful plant production. This chamber description represents a useful research tool to effectively produce uniformly or differentially multi-isotope labeled plant material for use in experiments on ecosystem biogeochemical cycling.

Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

This method explains how to build and operate a continuous 13C and 15N isotope labeling chamber for uniform or differential plant tissue labeling. Representative results from metabolic and structural labeling of Andropogon gerardii are discussed.

Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes ...

A Protocol for Conducting Rainfall Simulation to Study Soil Runoff

Rainfall is a driving force for the transport of environmental contaminants from agricultural soils to surficial water bodies via surface runoff. The objective of this study was to characterize the effects of antecedent soil moisture content on the fate and transport of surface applied commercial urea, a common form of nitrogen (N) fertilizer, following a rainfall event that occurs within 24&#160;hr&#160;after fertilizer application. Although urea is assumed to be readily hydrolyzed to ammonium and therefore not often available for transport, recent studies suggest that urea can be transported from agricultural soils to coastal waters where it is implicated in harmful algal blooms. A rainfall simulator was used to apply a consistent rate of uniform rainfall across packed soil boxes that had been prewetted to different soil moisture contents. By controlling rainfall and soil physical characteristics, the effects of antecedent soil moisture on urea loss were isolated. Wetter soils exhibited shorter time from rainfall initiation to runoff initiation, greater total volume of runoff, higher urea concentrations in runoff, and greater mass loadings of urea in runoff. These results also demonstrate the importance of controlling for antecedent soil moisture content in studies designed to isolate other variables, such as soil physical or chemical characteristics, slope, soil cover, management, or rainfall characteristics. Because rainfall simulators are designed to deliver raindrops of similar size and velocity as natural rainfall, studies conducted under a standardized protocol can yield valuable data that, in turn, can be used to develop models for predicting the fate and transport of pollutants in runoff.

A rainfall simulator was used to apply a consistent rate of uniform rainfall to packed soil boxes in a study of the fate and transport of urea, a nonpoint source environmental contaminant. Under uniform soil and rainfall conditions, antecedent soil moisture content exerted strong control over urea loss in surface runoff.

Rainfall is a driving force for the transport of environmental contaminants from agricultural soils to surficial water bodies via surface runoff. The ...

A CO2 Concentration Gradient Facility for Testing CO2 Enrichment and Soil Effects on Grassland Ecosystem Function

Continuing increases in atmospheric carbon dioxide concentrations (CA) mandate techniques for examining impacts on terrestrial ecosystems. Most experiments examine only two or a few levels of CA concentration and a single soil type, but if CA can be varied as a gradient from subambient to superambient concentrations on multiple soils, we can discern whether past ecosystem responses may continue linearly in the future and whether responses may vary across the landscape. The Lysimeter Carbon Dioxide Gradient Facility applies a 250 to 500 &#181;l L-1 CA gradient to Blackland prairie plant communities established on lysimeters containing clay, silty clay, and sandy soils. The gradient is created as photosynthesis by vegetation enclosed in in temperature-controlled chambers progressively depletes carbon dioxide from air flowing directionally through the chambers. Maintaining proper air flow rate, adequate photosynthetic capacity, and temperature control are critical to overcome the main limitations of the system, which are declining photosynthetic rates and increased water stress during summer. The facility is an economical alternative to other techniques of CA enrichment, successfully discerns the shape of ecosystem responses to subambient to superambient CA enrichment, and can be adapted to test for interactions of carbon dioxide with other greenhouse gases such as methane or ozone.

A CO2 Concentration Gradient Facility for Testing CO2 Enrichment and Soil Effects on Grassland Ecosystem Function

The Lysimeter Carbon Dioxide Gradient Facility creates a 250 to 500 &#181;l L-1 linear carbon dioxide gradient in temperature-controlled chambers housing grassland plant communities on clay, silty clay, and sandy soil monoliths. The facility is used to determine how past and future carbon dioxide levels affect grassland carbon cycling.

Continuing increases in atmospheric carbon dioxide concentrations (CA) mandate techniques for examining impacts on terrestrial ecosystems. Most ...

Spotting Cheetahs: Identifying Individuals by Their Footprints

The cheetah (Acinonyx jubatus) is Africa's most endangered large felid and listed as Vulnerable with a declining population trend by the IUCN1. It ranges widely over sub-Saharan Africa and in parts of the Middle East. Cheetah conservationists face two major challenges, conflict with landowners over the killing of domestic livestock, and concern over range contraction. Understanding of the latter remains particularly poor2. Namibia is believed to support the largest number of cheetahs of any range country, around 30%, but estimates range from 2,9053 to 13,5204. The disparity is likely a result of the different techniques used in monitoring.
Current techniques, including invasive tagging with VHF or satellite/GPS collars, can be costly and unreliable. The footprint identification technique5 is a new tool accessible to both field scientists and also citizens with smartphones, who could potentially augment data collection. The footprint identification technique analyzes digital images of footprints captured according to a standardized protocol. Images are optimized and measured in data visualization software. Measurements of distances, angles, and areas of the footprint images are analyzed using a robust cross-validated pairwise discriminant analysis based on a customized model. The final output is in the form of a Ward's cluster dendrogram. A user-friendly graphic user interface (GUI) allows the user immediate access and clear interpretation of classification results.
The footprint identification technique algorithms are species specific because each species has a unique anatomy. The technique runs in a data visualization software, using its own scripting language (jsl) that can be customized for the footprint anatomy of any species. An initial classification algorithm is built from a training database of footprints from that species, collected from individuals of known identity. An algorithm derived from a cheetah of known identity is then able to classify free-ranging cheetahs of unknown identity. The footprint identification technique predicts individual cheetah identity with an accuracy of &gt;90%.

The cheetah (Acinonyx jubatus) is an iconic, endangered species, but conservation efforts are challenged by habitat shrinkage and conflict with commercial farmers. The footprint identification technique, a robust, accurate and cost-effective image classification system, is a new approach to monitoring cheetahs.

The cheetah (Acinonyx jubatus) is Africa's most endangered large felid and listed as Vulnerable with a declining population trend by the IUCN1. It ranges ...

Vegetated Treatment Systems for Removing Contaminants Associated with Surface Water Toxicity in Agriculture and Urban Runoff

Urban stormwater and agriculture irrigation runoff contain a complex mixture of contaminants that are often toxic to adjacent receiving waters. Runoff may be treated with simple systems designed to promote sorption of contaminants to vegetation and soils and promote infiltration. Two example systems are described: a bioswale treatment system for urban stormwater treatment, and a vegetated drainage ditch for treating agriculture irrigation runoff. Both have similar attributes that reduce contaminant loading in runoff: vegetation that results in sorption of the contaminants to the soil and plant surfaces, and water infiltration. These systems may also include the integration of granulated activated carbon as a polishing step to remove residual contaminants. Implementation of these systems in agriculture and urban watersheds requires system monitoring to verify treatment efficacy. This includes chemical monitoring for specific contaminants responsible for toxicity. The current paper emphasizes monitoring of current use pesticides since these are responsible for surface water toxicity to aquatic invertebrates.

This article summarizes the design attributes and the effectiveness of treatment systems that treat urban stormwater and agriculture irrigation runoff to remove pesticides and other contaminants associated with aquatic toxicity.

Urban stormwater and agriculture irrigation runoff contain a complex mixture of contaminants that are often toxic to adjacent receiving waters. Runoff may ...

Design and Use of an Apparatus for Quantifying Bivalve Suspension Feeding at Sea

As shellfish aquaculture moves from coastal embayments and estuaries to offshore locations, the need to quantify ecosystem interactions of farmed bivalves (i.e., mussels, oysters, and clams) presents new challenges. Quantitative data on the feeding behavior of suspension-feeding mollusks is necessary to determine important ecosystem interactions of offshore shellfish farms, including their carrying capacity, the competition with the zooplankton community, the availability of trophic resources at different depths, and the deposition to the benthos. The biodeposition method is used to quantify feeding variables in suspension-feeding bivalves in a natural setting and represents a more realistic proxy than laboratory experiments. This method, however, relies upon a stable platform to satisfy the requirements that water flow rates supplied to the shellfish remain constant and the bivalves are undisturbed. A flow-through device and process for using the biodeposition method to quantify the feeding of bivalve mollusks were modified from a land-based format for shipboard use by building a two-dimensional gimbal table around the device. Planimeter data reveal a minimal pitch and yaw of the chambers containing the test shellfish despite boat motion, the flow rates within the chambers remain constant, and operators are able to collect the biodeposits (feces and pseudofeces) with sufficient consistency to obtain accurate measurements of the bivalve clearance, filtration, selection, ingestion, rejection, and absorption at offshore shellfish aquaculture sites.

A flow-through device for using the biodeposition method to quantify filtration and feeding behavior of bivalve mollusks was modified for shipboard use. A two-dimensional gimbal table built around the device isolates the apparatus from boat motion, thereby allowing the accurate quantification of bivalve filtration variables at offshore shellfish aquaculture sites.

As shellfish aquaculture moves from coastal embayments and estuaries to offshore locations, the need to quantify ecosystem interactions of farmed bivalves ...

Construction of a Compact Low-Cost Radiation Shield for Air-Temperature Sensors in Ecological Field Studies

Low cost temperature sensors are increasingly used by ecologists to assess climatic variation and change on ecologically relevant scales. Although cost-effective, if not deployed with proper solar radiation shielding, the observations recorded from these sensors will be biased and inaccurate. Manufactured radiation shields are effective at minimizing this bias, but are expensive compared to the cost of these sensors. Here, we provide a detailed methodology for constructing a compact version of a previously described custom fabricated radiation shield, which is more accurate than other published shielding methods that attempt to minimize shield size or construction costs. The method requires very little material: corrugated plastic sheets, aluminum foil duct tape, and cable ties. One 15 cm and two 10 cm squares of corrugated plastic are used for each shield. After cutting, scoring, taping and stapling of the sheets, the 10 cm squares form the bottom two layers of the solar radiation shield, while the 15 cm square forms the top layer. The three sheets are held together with cable ties. This compact solar radiation shield can be suspended, or placed against any flat surface. Care must be taken to ensure that the shield is completely parallel to the ground to prevent direct solar radiation from reaching the sensor, possibly causing increased warm biases in sun-exposed sites in the morning and afternoon relative to the original, larger design. Even so, differences in recorded temperatures between the smaller, compact shield design and the original design were small (mean daytime bias = 0.06 &#176;C). Construction costs are less than half of the original shield design, and the new design results in a less conspicuous instrument that may be advantageous in many field ecology settings.

With the advent of small, low-cost environmental sensors, it is now possible to deploy high-density networks of sensors to measure hyper localized temperature variation. Here, we provide a detailed methodology for constructing a compact version of a previously described custom-fabricated radiation shield for use with inexpensive thermochrons.

Low cost temperature sensors are increasingly used by ecologists to assess climatic variation and change on ecologically relevant scales. Although ...

Construction of a Low-cost Mobile Incubator for Field and Laboratory Use

Incubators are essential for a range of culture-based microbial methods, such as membrane filtration followed by cultivation for assessing drinking water quality. However, commercially available incubators are often costly, difficult to transport, not flexible in terms of volume, and/or poorly adapted to local field conditions where access to electricity is unreliable. The purpose of this study was to develop an adaptable, low-cost and transportable incubator that can be constructed using readily available components. The electronic core of the incubator was first developed. These components were then tested under a range of ambient temperature conditions (3.5 &#176;C - 39 &#176;C) using three types of incubator shells (polystyrene foam box, hard cooler box, and cardboard box covered with a survival blanket). The electronic core showed comparable performance to a standard laboratory incubator in terms of the time required to reach the set temperature, inner temperature stability and spatial dispersion, power consumption, and microbial growth. The incubator set-ups were also effective at moderate and low ambient temperatures (between 3.5 &#176;C and 27 &#176;C), and at high temperatures (39 &#176;C) when the incubator set temperature was higher. This incubator prototype is low-cost (&lt; 300 USD) and adaptable to a variety of materials and volumes. Its demountable structure makes it easy to transport. It can be used in both established laboratories with grid power or in remote settings powered by solar energy or a car battery. It is particularly useful as an equipment option for field laboratories in areas with limited access to resources for water quality monitoring.

This paper describes a method for building an adaptable, low-cost and transportable incubator for microbial testing of drinking water. Our design is based on widely available materials and can operate under a range of field conditions, while still offering the advantages of higher-end laboratory-based models.

Incubators are essential for a range of culture-based microbial methods, such as membrane filtration followed by cultivation for assessing drinking water ...

Combining Eye-tracking Data with an Analysis of Video Content from Free-viewing a Video of a Walk in an Urban Park Environment

As individuals increasingly live in cities, methods to study their everyday movements and the data that can be collected becomes important and valuable. Eye-tracking informatics are known to connect to a range of feelings, health conditions, mental states and actions. But because vision is the result of constant eye-movements, teasing out what is important from what is noise is complex and data intensive. Furthermore, a significant challenge is controlling for what people look at compared to what is presented to them.
The following presents a methodology for combining and analyzing eye-tracking on a video of a natural and complex scene with a machine learning technique for analyzing the content of the video. In the protocol we focus on analyzing data from filmed videos, how a video can be best used to record participants&#39; eye-tracking data, and importantly how the content of the video can be analyzed and combined with the eye-tracking data. We present a brief summary of the results and a discussion of the potential of the method for further studies in complex environments.

The objective of the protocol is to detail how to collect video data for use in the laboratory; how to record eye-tracking data of participants looking at the data and how to efficiently analyze the content of the videos that they were looking at using a machine learning technique.

As individuals increasingly live in cities, methods to study their everyday movements and the data that can be collected becomes important and valuable. ...

Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline

Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and shape of activated sludge flocs can indicate the conditions at the microscale, and also directly affect how well the sludge settles in a clarifier.
Particle size and shape are both misleadingly &#39;simple&#39; measurements. Many subtle issues, often unaddressed in informal protocols, can arise when sampling, imaging, and analyzing particles. Sampling methods may be biased or not provide enough statistical power. The samples themselves may be poorly preserved or undergo alteration during immobilization. Images may not be of sufficient quality; overlapping particles, depth of field, magnification level, and various noise can all produce poor results. Poorly specified analysis can introduce bias, such as that produced by manual image thresholding and segmentation.
Affordability and throughput are desirable alongside reproducibility. An affordable, high throughput method can enable more frequent particle measurement, producing many images containing thousands of particles. A method that uses inexpensive reagents, a common dissecting microscope, and freely-available open source analysis software allows repeatable, accessible, reproducible, and partially-automated experimental results. Further, the product of such a method can be well-formatted, well-defined, and easily understood by data analysis software, easing both within-lab analyses and data sharing between labs.
We present a protocol that details the steps needed to produce such a product, including: sampling, sample preparation and immobilization in agar, digital image acquisition, digital image analysis, and examples of experiment-specific figure generation from the analysis results. We have also included an open-source data analysis pipeline to support this protocol.

The size and shape of particles in activated sludge are important parameters that are measured using varying methods. Inaccuracies arise from non-representative sampling, suboptimal images, and subjective analysis parameters. To minimize these errors and ease measurement, we present a protocol specifying every step, including an open source software pipeline.

Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and ...