Swan(sea) Song – personal research during my six years at Swansea ... and bey...
Soil Remediation
1. 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?)
3. What is soil?
Soil as a Habitat
A 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.
10. 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.
17. “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.”
19. 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.
20. Singh et al 2011
Climate change and soil pathogens
21. 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.
22. 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
32. 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?
