Soil pollution and remediation: Pharmaceuticals / Biological pollution

Juan VillaRomero & Morgan Williams

What is soil? The soil microbiome: antibiotics and LGT Soil: problems and solutions Review of papers: antibiotics and antibiotic

resistance in soil Questions? Discussion (a step by step solution?)

What is soil?

What is soil?

Soil as a HabitatA soli habitat containing mineral soil particles (sand-Sa, silt-Si, and clay-C), organic matter (OM), water (W), plant root with root hairs (A), and soil organisms (bacteria-B. actlnomycetes-A, mycorrhizal spores and hyphae-My, hyphae of a saprophytic C fungus-H. a nematode-N,ciliate protozoa-CP, flagellate protozoa-FP, and a mite-M.) This soil can be a habitat of enormous complexity and diversity even over small distances. For example, the actual size of the soil in this drawing is < 1 mm in both directions yet may contain habitats that are acid to basic, wet to dry, aerobic to anaerob1c, reduced to oxidized, and nutrient-poor to nutrient rich. Realizing this complexity and diversity is the key to understanding soil microbiology. Original drawing by Kim Luoma. Used with permission.

The human microbiome

Nature Reviews Genetics 13, 260-270 (April 2012)

The Earth microbiome

The microbiome: LGT

Lateral Gene Transfer

LGT and microbial resistance

Soil: problems and solutions

Bacillus cereus gastroenteritis is an important food-borne disease worldwide, including an estimated 63,400 annual cases in the United States. B. cereus spores germinate within an animal host and enter soil through droppings or carcasses or they germinate on contact with organic material. Saprophytic growth occurs in soil. Cells/spores contaminate plant material and food processing areas (where spores persist, especially in biofilms) then cause disease after human consumption.

Pharmaceutical/biological pollution: the emergence of antibiotic resistance

Nature, 499, 7459 (July 2013)

Soil as Reservoir for Useful AntibioticsTuberculosis

Streptomycin

Streptomyces griseusSelman WaksmanRutgers UniversitySoil Microbiologist

Yersinia pestis

Physiology/Medicine 1952 Albert Schatz

Review of papers

Gerba & Smith, 2005.

Review of papers

Gerba & Smith, 2005.

“Agricultural antimicrobial drug is a major driver of antimicrobial resistance worldwide: 1) it is the largest use of antimicrobials worldwide; 2) much of the use of antimicrobials in agriculture results in subtherapeutic exposures; 3) drugs of every important clinical class are utilized in agriculture; 4) human populations are exposed to antimicrobial-resistant pathogens via consumption of animal products as well as through widespread release into the environment.”

“The problem is often conceptualized in terms of resistance to specific antimicrobials in pathogens of clinical importance, rather than ecologically in terms of reservoirs of resistance genes that may flow across the microbial ecosystem.”

“CAFOs are comparable to poorly run hospitals, where everyone gets antibiotics, patients lie in unchanged beds, hygiene is nonexistent, infections and reinfections are rife, waste is thrown out the window, and visitors enter and leave at will. ”

“New drugs can be licensed for agricultural use in advance of approvals for clinical use. In the case of virginiamycin, this FDA decision resulted in the emergence of resistance in human isolates prior to eventual clinical registration.”

“Resistance may continue even after antimicrobials are no longer present.”

“According to the USDA, confined food animals produce roughly 335 million tons of waste per year, more than 40 times the mass of human biosolids generated by publicly owned treatment works (7.6 million tons, 2005). In contrast to human biosolids, no treatment-process control requirements for pathogens have been established for animal waste prior to disposal, although levels of pathogens, as well as antimicrobial-resistant bacteria, are often higher than levels found in human feces.”

“At swine CAFOs that use ventilation systems resistant bacteria are detected in the air 30 m upwind and 150 m downwind.”

“Houseflies have been found to play a major role in the epidemiology of Campylobacter infections in communities near CAFOs. Rodents can also transfer pathogens in and out of animal houses. Wild avians are attracted to CAFOs and to the fields where poultry house waste is disposed because of the presence of spilled feed in this waste.”

“The risks of becoming infected by a resistant pathogen are higher in hospitals, but the source of resistance is greater outside the hospital, largely related to the size of the animal reservoir of resistance (which includes consumer meats and poultry).”

“From the scientific perspective, it is difficult to define what additional research is needed to support a change in public policy on antimicrobial use in agriculture.”

“There is a lack of attention to the importance of bacteria as living organisms, fundamentally different from chemicals; living organisms are capable of expanding in number and potential risk. Bacteria can transfer their toxic properties.”

CAFO/IFAP and antibiotic resistance

Nature, 499, 7459 (July 2013)

The survival of these pathogens in manure will largely depend on the temperature and moisture content of the materials. Other factors are oxygen level, pH, ammonium content, microbial competition, etc. In general, the higher the temperature and the longer the storage or treatment time of the manure, the less likely pathogens will survive.

Singh et al 2011

Climate change and soil pathogens

This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health.

Uncertainty...

“The National Research Council (Washington, DC. 2002) report “Biosolids applied to land” noted that additional scientific work is needed to reduce persistent uncertainty about the potential for adverse human health effects from exposure to biosolids.”

Gerba & Smith, 2005

“For all these reasons, it may not be possible to determine the attributable risk of antimicrobial use specific to agriculture or to the use of specific antimicrobials as feed additives—in terms of the overall incidence of resistant human infections, given a model that incorporates the notion of communities of humans and bacteria—as well as the importance of both gene flow and microbial transmission.”

Silbergeld et al., 2008

Questions? (20 minutes)

Eliminating antibiotic resistant microbes from soil can be achieved by following these steps:

1. Education and outreach? Reduce meat consumption? Reevaluate food requirement standards? Identify political stakeholders?

2. Reevaluate meat production protocols?

3. Economic analysis? Eliminating antibiotic use will harm industry? Reevaluate food subsidies?

4. Research: solutions and problems

5. Require prescription for the agricultural use of antibiotics

6. Introduce composting as a standard step for agricultural waste treatment?

7. Self-quarantine diseased populations?