Soils and Human Health

Transcription

1 Soils and Human Health National Geographic. Sept 2008 The nation that destroys its soil, destroys itself. - Franklin Delano Roosevelt

2 Haiti has lost its soil and the means to feed itself Rattan Lal, National Geographic Magazine Severe food shortages have led to consumption of cakes made of clay, salt and shortening

3 The United States has tremendous soil wealth. Of the two soil orders most suited for agriculture, the U.S. alone possesses 22% of the Earth s mollisols and 10% of its alfisols. Mollisol Alfisol Pennsylvania s Mahantango Creek watershed (alfisols)

4 Tolerable levels of soil erosion, even with inherently productive soils of Northern Hemisphere, contributes to sediment and nutrient transport to coastal dead zones (in red) Source: NASA Earth Observatory Mississippi River Basin Gulf of Mexico Dead Zone Chesapeake Bay 4

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6 Soils Harbor Tremendous Amounts of Biodiversity Numbers per gram in upper 1 meter Bacteria 2 x Archaea 1 x Fungi 1 x Protozoans 10,000 Nematodes 1,000 Microarthropods Bacteria 1 x 10 6 g -1 (1-8 m depth) Lower numbers for fungi Source: USDA Soil Biology Primer

7 Five Kingdoms but. Three Domains of Life The majority of Earth s genetic diversity is microscopic ANIMALS PLANTS FUNGI PROTOZOANS (4 Kingdoms) EUKARYOTES ARCHAEA BACTERIA M O N E R A 5 th Kingdom Carl Woese, Banfield group graphic

8 Traditional laboratory cultivation methods fail to recover 99% of soil bacteria observable under the microscope

9 Culturable soil microbes have been mined How to access the other 99%? Clear zone around bacterial colony producing an antifungal antibiotic

10 Soils have been the sources of 90% of disease-fighting drugs Alexander Fleming s discovery of penicillin in 1928 from a cultured soil fungus Actinomycetes (now called Actinobacteria) have been the primary source of antibiotics In 1943 Selman Waksman and his student discovered streptomycin the first antibiotic effective against tuberculosis from a culture of Streptomyces griseus Two days ago Nobel Prize in Physiology/Medicine shared by a Japanese and a U.S. scientist for discovery of Ivermectin (effective against debilitating human and animal parasites) from Streptomyces avermitilis Photos: inst.bact.wisc.edu

11 However.. Antibiotic resistance is rising Up to half of antibiotic use in humans is unnecessary or inappropriate Antibiotic use in animals also can be reduced Priority threats Carbapenem-resistant gram-negative bacilli Methycillin-resistant Staph aureus (MRSA) Vancomycin-resistant tuberculosis Hospital-acquired Clostridium difficile

12 Three known mechanisms for transfer of resistance genes to pathogens

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14 Four core actions to combat antibiotic resistance: Preventing Infections, Preventing the Spread of Resistance Tracking Improving Antibiotic Use/Stewardship Development of Drugs and Diagnostic Tests New antibiotics from undiscovered soil organisms

15 Isolation chip ( ichip ) for high-throughput microbial cultivation led to discovery of teixobactin D. Nichols et al. Appl. Environ. Microbiol. 2010;76: Source: The Scientist,

16 Microcolonies from ichip observed at 100X Teixobactin is produced by a new genus of gram-negative bacteria Binds to non-protein cell wall targets in gram-positive bacteria Effective against MRSA and tuberculosis Nichols et al Non-protein targets are less susceptible to mutation, so resistance expected to develop more slowly It took 30 years for resistance to develop to protein-targeting antibiotics like vancomycin development of resistance

17 Genomics Core Facility Providing next-generation DNA sequencing and genomic services to the Penn State community Illumina Hi-Seq Roche NimbleGen

18 Omics: collective characterization and quantification of biomolecules Genomics and Metagenomics Proteomics Metabolomics The suffix -ome applies to the subject being studied

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20 Soil Microbiome -- Analogous to the Human Microbiome Extracting DNA from soil is similar to forensic scientists extracting DNA from crime scene samples. Finding new DNA allows us to learn about uncultured, undiscovered organisms. Source: Coombs, A The Scientist

21 Soil Metagenomes: Measuring Biodiversity After Mineland Reclamation

22 -Omics Research in College of Ag Sci Veterinary and Biomedical Science Ecosystem Science & Management Andrew Patterson host-metabolite-microbiome Eric Harvill Pathogen genomes Chobi Debroy E. coli pangenomes John Carlson Tree genomics Food Science Jairam Vanamala Foodomics, foods and gut health Entomology Kelli Hoover Insect gut microbiomes

23 How much living biomass (bacteria, fungi, protozoans microinvertebrates) in an acre of soil? Assume dry weight of one acre of soil (at depth of 6 inches = 2,000,000 lbs) Assume 4% soil organic matter, of which 2% is live biota Answer: 1600 lbs microbial biomass

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