Critical Management Point: Crop Type

Critical Management Point: Crop Type

Transcript (with additional commentary)

In this study, lettuce and radishes grown in the greenhouse and field plot studies from critical control point 3, were harvested and analyzed.

[Monica Ponder, Department of Food Science and Technology, Virginia Tech]:
“So for our greenhouse study, where we’re growing different, a leafy green veg, lettuce, a root veg, radishes and another type of veg, a brassica, so a broccoli, we’re growing them in the greenhouse and we’re looking to see how many of the bacteria that are coming from compost from those cows that were earlier dosed with antibiotics, how much of that microbiota are transferred over to those growing plants.”

One recent study of a range of crops suggested some uptake of antibiotics in manure-amended soil, but at very low levels. Other studies have examined transfer from manure to crop and have suggested that transfer of certain antibiotic resistance genes between bacteria may be enhanced in the rhizosphere, where the plant roots exist.

However, there is a lack of information on antibiotic metabolites and how compost-soil interactions might influence bioavailability of the antibiotics, antibiotic resistant bacteria, and antibiotic resistance genes.

Lettuce, radishes, and broccoli were selected as models in this study because they are commonly consumed raw and their organic production uses composted manure.

In the lab, we took bacterial samples from the soil and plant surfaces and grew them in culture plates that are partially filled with nutrient agar, to provide the space and nutrients necessary for the bacteria to replicate and incubate.

Plates were then prepared with different types of antibiotics added to the media in order to estimate the numbers of resistant bacteria.

Another procedure, called quantitative polymerase chain reaction, was used to count the number of antibiotic resistance genes corresponding to the different antibiotics used in this study.

We looked at determining if residual antibiotics left in compost can lead to more resistant bacteria on vegetables and if composting presents advantages over raw manure for reducing the spread of antibiotic resistance. This study will provide guidance on three objectives:

  • How composting affects plant uptake of antibiotics, antibiotic resistant bacteria, and antibiotic resistance genes
  • If certain types of crops (radishes, lettuce, broccoli) are more susceptible to being colonized by antibiotic resistant bacteria
  • And, if certain soil types can help mitigate tendencies of vegetables to be colonized by antibiotic resistant bacteria

Glossary of Terms

  • Antibiotic drug – Antibiotics are compounds that kill or slow the growth of bacteria and are used to treat or prevent infection.
  • Antibiotic metabolites – Break-down products that are formed as antibiotic parent molecules are degraded. Metabolites are generally not fully functional compounds, but are results of metabolism and other degradation processes.
  • Antibiotic resistance genes – Pieces of DNA carried by bacteria that encode functions that allow bacteria to survive and grow in the presence of antibiotics.
  • Antibiotic resistant bacteria – Bacteria that are not controlled or killed by an antibiotic with a spectrum that includes that type of bacteria.  An antibiotic spectrum is the range of bacteria susceptible to that drug. (CDC, Antibiotic Resistance,
  • Bioavailability – The proportion of a substance that is able to enter an organism unchanged and have an active effect, i.e., of the quantity of nutrient applied to a plant, how much is taken up and integrated by the plant?  If a substance is more bioavailable, it is more readily taken up and used by the plant.
  • Crop uptake – Plants taking in materials primarily through roots, leaves, or other tissue.  Uptake could include nutrients like nitrogen or phosphorus, agricultural chemicals, water, air, or any number of soil additives.
  • Gene transfer – The process by which bacteria share genes. Antibiotic resistance genes are especially prone to being shared by bacteria. Gene transfer processes include: transformation uptake of naked DNA, conjugation (bacterial mating), and transduction (virus-mediated gene transfer).
  • Inoculation – Deliberate introduction of small amounts of microorganisms to allow them to grow. In this case, bacteria are swabbed onto the surface of an agar plate and allowed to multiply in order to count resulting colonies.
  • Metabolites – Small molecules that are intermediate products after a drug is broken down by the body. They may or may not retain properties of the parent compound.
  • Microbiota or microorganisms – The ecological community of microscopic living organisms that share one space. These microorganisms could include bacteria, viruses, fungi, root hairs, other one-celled organisms, or small multi-celled organisms.
  • Polymerase chain reaction – A technique used in molecular biology where a single copy or a few copies of a piece of DNA is amplified to produce millions of copies that are then read and analyzed. (NCBI, PCR: )


  • Jechalke, S., Kopmann, C., Rosendahl, I., Groeneweg, J., Weichelt, V., Krogerrecklenfort, E., Brandes, N., Nordwig, M., Ding, G.C., Siemens, J., Heuer, H., Smalla, K. 2013. Increased abundance and transferability of resistance genes after field application of manure from sulfadiazine-treated pigs. Appl. Environ. Microbiol. 79, 1704-1711.
  • Kang, D.H., Gupta, S., Rosen, C., Fritz, V., Singh, A., Chander, Y., Murray, H., Rohwer, C. 2013. Antibiotic uptake by vegetable crops from manure-applied soils. J. Agric. Food Chem. 61, 9992-10001.
  • Marti, R., Scott, A., Tien, Y.C., Murray, R., Sabourin, L., Zhang, Y., Topp, E. 2013. Impact of manure fertilization on the abundance of antibiotic-resistant bacteria and frequency of detection of antibiotic resistance genes in soil and on vegetables at harvest. Appl. Environ. Microbiol. 79, 5701-5709.