Assessment of method of photo analysis for demonstrating soil quality


The use of livestock manure as a soil amendment to benefit soil health by improvements to soil physical, chemical, and biological properties, has been documented. However, quantification of the impact of improved soil health metrics on nutrient cycling has lagged. The soil your undies experiment has been implemented in the past to visually demonstrate microbial activity (Figure 1). However, this demonstration is seldom quantified, and does not have the capacity to statistically show that the effects of different management practices are distinct. The goal for this study was to quantify the degradation of fabric on a similar experiment, using cotton fabric on agricultural soils through photographic editing software. This study was designed to assess a visual method for quantifying carbon cycling in soil, observed through the degradation of buried organic materials.

Figure 1. Soil your undies soil health demonstration. Credit Clackamas Soil and Water Conservation District.

What Did We Do?

White, 100% cotton fabric cloths were cut into 29.21 × 29.84 cm (871.62 cm2) (11.5 x 11.75 in, 135 in2) pieces and placed flat inside a non-degradable mesh bag (48 cm × 48 cm, 18.9 in x 18.9 in). Sixty of the mesh bags were buried at 5 cm (2 in) depth in a field planted with corn in May of 2021 (Figure 2). The sixty bags were arranged in 12 plots to which one of three soil treatments (swine slurry, swine slurry + woodchips, and control plots with no amendments) with four replications per treatment were also applied. Swine slurry was applied at a rate of 39,687.06 L-ha-1 (4,242 gal-ac-1) and woody biomass was applied at a rate of 21.52 Mg-ha-1 (9.6 tons-ac-1).

Figure 2. Fabric and mesh bag burial in research plots

Five times during the growing season (25, 54, 81, 99 and 128 days after establishment), one bag was retrieved from each plot and returned to the lab for analysis. For each bag, soil was gently removed from the surface of the mesh and then the bag was cut open to observe the cotton fabric remaining. All the fabric pieces were photographed after retrieval. Photographs of the fabric were taken with an iPad mounted on a tripod. Fabric samples were photographed in a premeasured area of 29.21 × 29.84 cm (11.5 x 11.75 in) on a black surface (Figure 3).

Figure 3. Fabric sample placement inside pre-measured area (29.21 × 29.84 cm) for photographing

Manual evaluation of percent fabric degradation for each sample was performed by overlaying a clear plastic grid (Figure 4) with primary graduations (darker lines) of 2.54 cm (1 in) and secondary graduations (lighter lines) of 6.4 mm (0.25 in) on fabric samples and counting grid squares that were void of fabric.

Figure 4. Grid overlayed on fabric sample for manual evaluation of percent fabric degradation

Each photograph was assessed using Adobe Photoshop 2020 and the free license program ImageJ. Briefly, each image was opened in the respective program and the initial fabric area (871.62 cm2) (135 in2) was delineated in the program, based on the premeasured area included in the photo to set a scale for the degradation measurement. The image was converted to black and white, and brightness and contrast were adjusted as needed to remove glare on the black background that might be misread by the program as fabric. Then, all the pixels within a specific color range – which was previously defined as fabric – were selected using the native editing tools in the two programs and this area was compared to the pixels in the initial fabric area to determine the percentage of fabric remaining.

What Have We Learned?

The three methods for estimating the area of the fabric did not show significant differences among each other, which means estimates of fabric degradation obtained with Photoshop and Image J accurately reflect manual hand counts, suggesting that these are reliable visual methods for determining the area of the remaining area of fabric (Figure 5, 6).

Figure 5. Linear regression model for degradation estimation via Photoshop relative to degradation value obtained by hand count
Figure 6. Linear regression model for degradation estimation via ImageJ relative to degradation value obtained by hand count

Future Plans

Future work will seek to validate this method according to standard measures of soil health and biological activity and ensure that the method has enough sensitivity to demonstrate statistical differences between soil treatments. Future studies should also focus on making the process of area estimation with the software an easier, less laborious process. Creating a cellphone app to determine degradation quickly and without the need for a computer could increase the adoption of the fabric degradation assessment method in field settings.


Amy Schmidt, Associate Professor, University of Nebraska-Lincoln

Corresponding author email address

Additional authors

Karla Melgar Velis, Graduate Research Assistant, University of Nebraska-Lincoln

Mara Zelt, Research Technologist, University of Nebraska-Lincoln

Andrew Ortiz Balsero, Undergraduate Research Assistant, University of Nebraska-Lincoln


Funding for this study was provided by the Nebraska Environmental Trust and Water for Food Global Institute at the University of Nebraska-Lincoln. Much gratitude is extended to collaborating members of the On-Farm Research Network, Nebraska Natural Resource Districts, Nebraska Extension Agents and Michael Hodges and family for providing the land, manure, and effort for this research project. Much appreciation to members of the Schmidt Lab who supported field and laboratory work: Juan Carlos Ramos Tanchez, Nancy Sibo, Andrew Lutt, Seth Caines and Jacob Stover.

Antibiotic Resistance in Manure-Amended Agricultural Soils

Report on research conducted at the University of Nebraska, originally printed in the 2021 Nebraska Beef Cattle Report.


Manure application to agricultural land benefits soil health and agronomic yields. However, as antibiotic resistance becomes a more serious threat to public health, there is concern that antibiotic resistance originating from livestock manure could impact human health through contamination of the environment or food. This study sought to quantify this risk by monitoring concentrations of antibiotic-resistant bacteria and genes in fallow soil during the period of October through April, representing fall manure application through spring planting. Resistance to three common antibiotics – tylosin, azithromycin, and tetracycline – was monitored following application of fresh, stockpiled, or composted beef feedlot manure, or inorganic fertilizer. Overall, concentrations of all monitored resistant bacteria were below the detection limit for enumeration. Results indicate that while all the manure treatments increased at least one measure of antibiotic resistance during the sampling period, by the final sampling day antibiotic resistance prevalence and concentrations in manured plots were not significantly different from soil receiving no fertilizer treatments  Continue reading “Antibiotic Resistance in Manure-Amended Agricultural Soils”

Microarthropods as Bioindicators of Soil Health Following Land Application of Swine Slurry

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As producers of livestock and agricultural crops continue to focus significant efforts on improving the environmental, economic, and social sustainability of their systems, increasing the utilization of livestock manure in cropping systems to offset inorganic fertilizer use benefits both sectors of agriculture. However, promoting manure based purely upon nutrient availability may not be sufficient to encourage use of organic versus inorganic fertilizer. The value of livestock manure could increase significantly with evidence of improved soil fertility and quality following manure application. Therefore, understanding the impact of manure addition and application method on both soil quality and biological health is an important step towards improving the value and desirability of manure for agricultural cropping systems.

For edaphic ecosystems, collection, analysis, and categorization of soil microarthropods has proven to be an inexpensive and easily quantified method of gathering information about the biological response to anthropogenic changes to the environment (Pankhurst et al., 1995; Parisi et al., 2005). Arthropods include insects, crustaceans, arachnids, and myriapods; nearly all soils are inhabited by a vast number of arthropod species. Agricultural soils may contain between 1,000 and 100,000 arthropods per square meter (Wallwork, 1976; Crossley et al., 1992; Ingham, 1999). Soil microarthropods show a strong degree of sensitivity to land management practices (Sapkota et al., 2012) and specific taxa are positively correlated with soil health (Parisi et al., 2005). These characteristics make soil microarthropods exceptional biological indicators of soil health.

This study focused on assessing the chemical and biological components of soil health, described in terms of soil arthropod population abundance and diversity, as impacted by swine slurry application method and time following slurry application.

What did we do? 

A field study was conducted near Lincoln, Nebraska from June 2014 through June 2015 on a site that has been operated under a no-till management system with no manure application since 1966. Experimental treatments included two manure application methods (broadcast and injected) and a control (no manure applied).

Soil samples were collected twelve days prior to treatment applications, one and three weeks post-application of manure, and every four weeks, thereafter, throughout the study period. Samples were not collected during winter months when soil was frozen.

Two types of soil samples were collected. Samples obtained with a 3.8-cm diameter soil probe were divided into 0-10 and 10-20 cm sections for each of the plots for nutrient analysis at a commercial laboratory. Samples measuring 20 cm in diameter and 20 cm in depth, yielding a soil volume of 6,280 cm3, were stored in plastic buckets with air holes in the lids, placed in coolers with ice packs, and transported to the University of Nebraska-Lincoln West Central Research & Extension Center in North Platte, Nebraska within 12 h of collection. These samples were then transferred to Berlese-Tullgren funnels for extraction of arthropods, a commonly used technique to assess microarthropods in the soil (Ducarme et al., 2002). A 70% ethanol solution was used to preserve the organisms for later analysis.

The QBS method of classification was employed to assign an eco-morphological index (EMI) score on the basis of soil adaptability level of each arthropod order or family (Parisi et al., 2005). Preserved arthropods from each soil sample were identified and quantified using a Leica EZ4 stereo microscope (Leica Biosystems, Inc., Buffalo Grove, IL) and a dichotomous key (Triplehorn and Johnson, 2004). Arthropods were classified to order or family based on the level of taxonomic resolution necessary to assign an EMI value as described by Parisi et al. (2005). For some groups, such as Coleoptera, characteristics of edaphic adaptation were used to assign individual EMI scores.

The impacts of swine slurry application method and time following manure application on soil arthropod populations and soil chemical characteristics was determined by performing tests of hypotheses for mixed model analysis of variance using the general linear model (GLM) procedure (SAS, 2015). The samples were tested for significant differences resulting from time and treatment, as well as for variations within the treatment samples. Following identification of any significant differences, the least significant differences (LSD) test was employed to identify specific differences among treatments. P <0.05 was considered statistically significant.

What have we learned? 

A total of 13,311 arthropods representing 19 orders were identified, with Acari (38.7% of total arthropods), Collembola: Isotomidae (26.8%), Collembola: Hypogastruridae (10.4%), Coleoptera larvae (1.6%), Diplura (1.2%), Diptera larvae (0.9%), and Pseudoscorpiones (0.6%) being the most abundant soil-dwelling taxa. These taxa had the greatest relative abundance in samples throughout the study and were, therefore, chosen for statistical analysis of their response to manure application method and time since application.

The most significant responses to application method were found for collembolan populations, specifically for Hypogastruridae and Isotomidae. However, Pseudoscorpiones were also significantly affected by application method. Time following slurry application had a significant impact on most of the analyzed populations including Hypogastruridae, Isotomidae, mites, coleopteran larvae, diplurans, and dipteran larvae. The positive response of Hypogastruridae and Isotomidae collembolans to broadcast swine slurry application was likely due to the addition of nutrients (in the form of OM and nitrates) to the soil provided by this form of agricultural fertilizer.

Future Plans   

Research focused on the role of livestock manure in cropping systems for improved soil quality and fertility is underway with additional soil characteristics being monitored under multiple land treatment practices with and without manure.

Corresponding author, title, and affiliation       

Dr. Amy Millmier Schmidt, Assistant Professor, University of Nebraska – Lincoln

Corresponding author email

Other authors   

Nicole R. Schuster, Julie A. Peterson, John E. Gilley and Linda R. Schott

Additional information               

Dr. Amy Millmier Schmidt can also be reached at (402) 472-0877.

Dr. Julie Peterson, Assistant Professor of Entomology, University of Nebraska – Lincoln can be reached at (308) 696-6704 or


Eric Davis, Ethan Doyle, Mitchell Goedeken, Stuart Hoff, Kevan Reardon, and Lucas Snethen are gratefully acknowledged for their assistance with field data collection. Kayla Mollet, Ethan Doyle, and Ashley Schmit are acknowledged for their assistance with data processing. This research was funded, in part, by faculty research funds provided by the Agricultural Research Division within the University of Nebraska-Lincoln Institute of Agriculture and Natural Resources.


The authors are solely responsible for the content of these proceedings. The technical information does not necessarily reflect the official position of the sponsoring agencies or institutions represented by planning committee members, and inclusion and distribution herein does not constitute an endorsement of views expressed by the same. Printed materials included herein are not refereed publications. Citations should appear as follows. EXAMPLE: Authors. 2017. Title of presentation. Waste to Worth: Spreading Science and Solutions. Cary, NC. April 18-21, 2017. URL of this page. Accessed on: today’s date.

Manure & Soil Health: Roundtables to Advance our Understanding of the State of the Science

Farmers and ranchers are becoming increasingly aware of the importance of soil quality/health to the productivity and sustainability of their agricultural system. Research and field observations have demonstrated that carefully managed manure applications can contribute to improved soil quality with limited environmental and social risks. However, a comprehensive assemblage of outputs and conclusions from research studies, field trials, soil labs databases, and other sources has never been developed. Therefore, the purpose of the initiative, Manure & Soil Health: Understanding and Advancing the State of the Science, is to assemble current knowledge on this topic, make it available to those influencing manure and land management decisions, and use it to inform and facilitate future research and service needs. The intent of the roundtables is to improve our understanding of: current knowledge, critical and emerging issues for which there are knowledge gaps, and information needs of farmers and their advisors.

What’s A Roundtable?

The four, hour-long roundtables consisted of a panel discussion with experts who were asked to summarize their current understanding of topics. Each panel also included a practitioner who shared perspectives on critical information needs of farmers and advisors and field experiences relative to use of manure. Panels were moderated to encourage interaction with audience. Roundtable participants were invited to ask questions of panelists and share expertise and experience.

When Were The Roundtables Held?

Date/Time Topic Panel Experts

February 9, 2017

Manure and Soil Health Testing Bianca Moebius-Clune
Donna Brandt
Russell Dresbach
Geoff Ruth

February 16, 2017

Manure and Soil Biology Rhae Drijber
Michele Soupir
Dr. Jonathan Lundgren

February 23, 2017

Manure and Soil Erosion, Runoff, and Losses Nathan Nelson
John Gilley
Mike Kucera
Andy Scholting

March 9, 2017

Manure and Cover Crops Tim Harrigan
Barry Fisher
Heidi Johnson
Sarah Carlson

Manure and Soil Biology

In the Manure and Soil Biology roundtable, our goal was to discover the influence of manure, both positive and negative, on soil biology. We discussed if certain fields will produce more soil biology benefits than others and whether timing of application affects these benefits. Finally, we debated whether we can derive an economic value for manure beyond its nutrient value. Field experiences and observations related to the value of manure as well as what farmers still need related to soil building with manure were reviewed. This dialogue was the second in a four part series discussing the current state of our knowledge relative to manure’s impact on soil health.

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Rhae Drijber, University of Nebraska – Lincoln

Michelle Soupir, Iowa State University

Jonathan Lundgren, Blue Dasher Farms


Other Manure and Soil Health (MaSH) Information