Microbiology 2016-10-20T02:08:33+00:00

The microbiology discipline also incorporates a number of integrated fields involving: biology, bioremediation, toxicology, epidemiology, and remediation. Because bioremediation has been shown to be effective in environmental cleanups throughout the country and overseas, many projects have claimed successes; many are successful but many are a result of volatilization. In some cases, the improvement may not be due to bioremediation alone.

Laboratory chemical analyses are used to characterize subsurface conditions, and a familiarization with biological processes in hostile, subsurface environments is important to resolve the numerous, complex issues involved in bioremediation. This also includes the need to address hydrogeology issues to characterize the subsurface for use in designing effective bioremediation programs.

Microbiology also comes into play in cases involving ground-water contamination by bacteria and viruses of potential harm to humans, i.e., certain “new” strains of Escherichia coli (O157:H7) have been shown to be especially harmful to young children and older persons with damaged immune systems. Contaminant source control and water well location play an important role in providing safe drinking water in the rural setting. Even ground-water supplies from town wells must be monitored carefully. Recent examples of such problems were found in Ontario (Canada) and in New York.

More recently, black mold has begun to present potential problems to homeowners. In a growing number of cases, some black mold species present serious health risks. Exposure lawsuits are increasing in number.

Refinements and enhancement of remediation technologies continue to produce a variety of new techniques for optimizing in-situ destruction or physical extraction for ex-situ destruction. Development and implementation of these techniques requires flexible designs and flexible, responsive management styles that can adapt to new information to expedite the remediation process.

Why Water-Supply Microbiology?

  • Detection and Enumeration of Potential Pathogens
  • Advisory for Disinfection
  • Insight into Microbial Fouling and Degradation of Water Quality
  • Bacteria (characteristics, pathogens)
  • taste, odor appearance issues
  • production & biofouling issues
  • Viruses (characteristics, pathogens)
  • Protozoa (characteristics, pathogens)
  • Treatment issues (surface/ground water)
  • Distribution issues
  • Conclusions

Direct Bacteria Count on Core Samples

Subsurface Bacteria:

  • Most widely distributed life forms
  • Total counts 100,000 to 10,000,000/gram dry soil
  • Normally 0.4-14.0 µm long/ 0.2-1.2 µm wide (starved forms smaller)
  • Predominantly Gram negative filamentous forms and spores rare
  • Types vary with depth; different from surface stains
  • Many species unidentified and uncharacterized
  • Diversity lower than surface but does not decrease with depth.

Resident Bacteria Genera in Ground Water:


Drinking Water CCL Microorganisms:

Aeromonas hydrophila
Helicobacter pylori

Mycobacterium avium-intracellulare (MAC)
Acanthamoeba (guidance for contact lens wearers)
Microsporidia (Enterocytozoon & Septata)
Cyanobacteria and other freshwater algae, toxins, etc.

Bacterial Diseases Associated with Drinking Water (Ground Water & Surface Water):

  • Historical: Typhoid fever
  • Current: Campylobacteriosis, Cholera, Gastroenteritis ( E. coli & HUS), Shigellosis, Salmonellosis, Tularemia, Legionnaires’, etc.
  • Future: Aeromonas hydrophila (food borne, occurs independent of fecals, diarrhea & dysentery), Helicobacter pylori (peptic ulcers, gastritis, gastric cancer), Mycobacterium avium-intracellulare (respiratory).

Issues Related to Taste, Odor, and Appearance of Drinking Water:

  • Sulfate-reducing bacteria: corrosion, “rusty” water, offensive odors (Desulfovibrio desulfuricans).
  • Well bore clogging, reduced production, increased energy and operating costs (iron, slime bacteria Clonothrix, Crenothrix, Leptothrix, Gallionella).
  • Soluble metals produced from microbial reduction of oxides, hydroxides and sulfidesferrous (reduced iron) manganous (reduce manganese).
  • Chlorination historical treatment

Norwalk-type virus (calicivirus)
Electron Micrograph, Bar at lower right= 0.1 µm


  • Inactive outside of a living host cell
  • Size 0.02-0.09µm
  • Contain only one type of nucleic acid (RNA or DNA)
  • Waterborne disease-types have protein coat for protection from harsh environments
  • Existing disinfectants remain effective
  • Historical: Polio virus
  • Current: Viral gastroenteritis: Norwalk, calicivirus, Viral Hepatitis A
  • Future: (CCL), ssRNA group, recent outbreaks, occurrence in finished waters.

Giardia lamblia (cycts)
White Bar Above = 1 µm


  • Common in surface water, much larger than bacteria and viruses
  • Form cysts for protection from harsh environments including disinfectants
  • Life cycles may include alternate host, reservoirs
  • Rare in subsurface, generally as invaders
  • Historical: Amebic dysentery, amebiasis: Entamoeba sp.
  • Current: Cryptosporidiosis: Cryptosporidium parvum Giardiasis: Giardia lamblia; filtration
  • Future: Microsporidia (Enterocytozoon & Septata) chlorination and filtration ineffective.

Cryptosporidium parvum (oocysts)
White Bar at Right = 1 µm

Life Cycle of Cryptosporidium parvum

Typical Treatment Processes:

Surface-Water Sources: Ground-Water Sources:
Screening? Yes Not Required
Coagulation/ rapid mixing? Yes Not Required
Flocculation? Yes Not Required
Sedimentation? Yes Not Required
Filtration? Yes Some Occasions
Disinfection? Always Recommended
Clear holding tank? Yes Yes, generally
Distribution system? O, M & D Yes

Indoor Air Quality and Assessment of Mold and Mildew Impacts

In the past few years, indoor air quality and assessments of mold and mildew impacts have received widespread attention in home repair and in litigation. The typical assessments require only a few hours inspecting the residence, which usually includes:

  1. The assessment starts with a visual observation and interpretation of the conditions present. A digital photographic record of observations in the home focuses on the signs of water infiltration and fungal growth.
  2. Samples are collected for culture and for on-site analysis using the HMB IV instrument. The device is capable of quantifying viable, vegetative fungal and bacterial biomass in a variety of matrices, e.g., plaster board, particleboard, paneling, wallpaper, carpet, and many other media. Samples collected from 6-10 specific locations will usually provide a temporal history of airborne biomass present in the residence. Samples containing high activity then can be applied to an agar growth medium for subsequent culture and identification in the laboratory.
  3. Then, 15-20 nutrient agar petri plates are placed in the residence for an exposure period of one hour. The petri plates collect airborne particles and provide the growth medium for germination and growth of both fungal and bacterial propagules. The interpretations of the growth present in the deposition plates provide an indication of the distribution of the airborne biological load present in the residence. The placement of the plates supports observations in 1) and may reveal the source or center of contamination in the home.
  4. Statistical analysis is conducted on the data produced from the deposition plates and from the HMB IV analyses. This provides an understanding of the relative importance of the data gathered.
  5. Predominant colony types are characterized macroscopically and further evaluated microscopically for identification of the fungi to the genus level. A trinocular research microscope capable of up to 1,600x magnification is used to visualize, for identification, the various fungal hyphae and spore-bearing structures stained with lacto-phenol cotton blue to facilitate ID, and
  6. A photographic record is generated of the fungal and bacterial colonies present on each plate exposed.

Following the assessment, about three weeks are required to complete laboratory incubation, data collection, analysis, identifications, and report preparation. The report usually consists of about 15-20 pages containing information suitable for guiding remediation efforts or for litigation support. Cladosporium, Penicillium, Aspergillus, Curvularia, and Alternaria species are commonly found in many locations. However, Stachybotrys species have also been identified in a number of locations.

Laboratory chemical analyses are often used to characterize materials found in residential, commercial and subsurface conditions, and a familiarization with biological processes in hostile subsurface environments is important to resolve complex issues concerning clean-up and associated bioremediation. This activity also often includes hydrogeologic issues to characterize the subsurface for designing effective bioremediation programs.


  • Microbiological agents are a major cause of disease and death in the world.
  • In U.S., $300 Million to $3 Billion in hospital costs attributed to waterborne
    pathogens; still 20-30 waterborne outbreaks/year.
  • Safe Drinking Water Amendments (SDWA), Information Collection Rule (ICR): 18 month monitoring period for microbial contamination beginning July, 1997.
  • Continued disinfection with halogens? production of halogenated TOC carcinogens.
  • Efficacy of alternate disinfectants? (UV, ozone, etc.).
  • Filtration: unit size vs. pore size?
  • Water reuse programs?

The I2M Principals responsible for this discipline’s activities are:

Michael D. Campbell, P.G., P.H.

Richard C. Bost, P.E., P.G.

Feel free to contact us to discuss your project needs or to arrange a speaking engagement by one of our Associates for a professional training session, a technical conference, society meeting, or for a graduation ceremony or other function where the knowledge and experience of our Associates may be of interest to your group.

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I2M Associates, LLC offers experienced engineers, geologists, hydrogeologists, and other scientists with many years in environmental assessments, including remediation management, mineral exploration and mining, project management, and mergers and acquisitions. Related areas of expertise include forensic and feasibility studies in the environmental and mining industries, and environmental site assessments, due diligence assessments, and impact assessments in addition to brownfield redevelopment and management (as well as grant application assistance) in the U.S, and for state and the U.S. governments, and the legal community around the U.S.

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