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by Stuart A. Smith, MS, CGWP, Ground Water Science Copyright © 1998-2015 Stuart Smith, all rights reserved. You may copy for personal reference, but please credit the source (author and URL). The NGWA’s site has a biofouling article with several excerpts from this work.

There are bacteria in the well?

While not the surprise it was to people perhaps a decade or so ago, microorganisms (mostly - but not all - bacteria) native to aquifer formations are found in wells. Generally, they occur in natural communities on surfaces, known as biofilms. Well biofilms are just one example of the natural tendency of microorganisms to live this way.

How do these microorganisms affect the water?

In addition to health-related problems, bacteria and other microorganisms may affect water quality and contribute to clogging, corrosion, and changes in water treatment performance, as well as unpleasant taste and odor.

This "primer" is intended to serve as a basic reference for sources and routes of microbial occurrence in wells, how to test for and minimize microbial growth, and how to manage it if biofouling becomes a problem.

Where do the microorganisms (including bacteria) come from?

Once upon a time, experts in public health and water supply used to think that the subsurface was some kind of giant filter that trapped microorganisms before they could get to ground water, resulting in an effectively sterile water resource unless microorganisms were introduced to the well from the outside – via undesirable pathways to the well intake, or by well service activities or other accidental means through the top of the well such as small animals that fall into the well.

We now know that 1) that view was due to primitive methods and 2) many types of microorganisms are native or adapted to saturated sediments and rock, and are indeed present in significant numbers in most water supply aquifers, even deep formations.

Bacteria have even been found in oil field brines from great depth, and in cores from rock hundreds of meters deep in locations never penetrated by a drill before. Given time and a route (and soil and rock provide plenty of both), bacteria and protozoa will migrate into and take up housekeeping in an aquifer. The environment is really rather nice: quiet, lots of surface area, often-adequate carbon sources, and moderate temperatures with little environmental change.

Yes, mice and crickets make unfortunate choices when seeking a warm place to sleep. And yes, drillers and pump installers/servicers can also introduce microorganisms during their activities. "Non-native" coliform bacteria, or "protozoa" (or archezoa) of potential health concern such as Giardia and Cryptosporidium are most likely introduced from the surface. However, these "accidental" routes should not be considered the primary source of native microorganisms. There are protozoa native to ground water, by the way. Stygofauna, small aquatic animals, are found in some aquifers, especially chalk and limestone.

There is no practical way at present to say for certain what is the source for many microorganisms in any one well – maybe someday, but not yet. Progress is being made in tagging the sources of certain bacteria such as coliforms, for example, do they come from hogs, cattle or people?

Special mention: Methanogens

Just like it sounds, these are microbes that generate methane. They are members of the Superkingdom Archaea, that is, single-cell microbes that are neither Bacteria nor Eukaryotes. They are the direct or indirect source of the bulk of the planet's methane.

What is the "iron bacteria" problem?

Better described as iron biofouling, the problem popularly known as "iron bacteria" is both complex and widespread. It is a natural phenomenon – microorganisms interacting with metals and minerals in their environments. Iron biofouling affects wells and water systems around the world in all sorts of aquifer environments: contaminated and pristine and climates arctic to tropical. In some places it causes great damage, in others it is considered a minor nuisance.

slime"Iron bacteria" is one type of biofouling among several, including the characteristic white sulfur slime of sulfur springs. Manganese, and even aluminum biofouling are also found in ground water systems.

Iron and other biofouling consists of biofilms which include living and dead bacteria, their sheaths, stalks, secretions and other leavings, and embedded metal oxihydroxide particles.

Bacterial iron can usually (but not always) be distinguishable visually from purely mineral iron incrustation by its soft, feathery or slimy appearance, and microscopically by the presence of bacterial structures and distinct mineral types. Under the microscope you can see the long, thin filaments or twisting stalks of various types by which microbiologists name the "iron bacteria". Some of these are actually manganese bacteria, and most of the following applies to manganese also. Iron particles are often incrusted on the bacterial structures. However, the bacteria present consist of many types, and the classy looking filaments and stalks in the textbooks may be entirely absent. These biofilms are natural and usually harmless. Natural iron biofouling often acts as a preliminary iron filter in wells and therefore can serve a positive function as well.

mixed iron-related biofilmBiofouling can be a nuisance, however. Mineral iron encrustation without the involvement of bacteria is rare in normal ground water environments. Generally, biological action is the cause of iron build up in wells and pipes (and the sole cause of manganese build up). Bacterial iron may build up quickly compared to mineral incrustation. In addition to causing problems in wells, the bacteria may colonize tanks and water treatment devices, as well as spring outfalls.

Biofouling generally causes side effects such as slight and intermittent sulfide odor, breakthroughs of red or brown water, and pitting-type corrosion of iron and steel.

What causes bacterial iron buildup?

The root causes are the presence of the bacteria themselves, dissolved or complexed iron or (sometimes) manganese or sulfur species, and an environment that encourages bacterial survival and growth.

Factors that may cause natural iron (or manganese) biofouling to be worse than it might be otherwise include: inappropriate well, filter or plumbing design or material choice, or construction, poor choices in water treatment, and well use patterns. Design, material selection, or construction flaws may cause corrosion, extra chemical oxidation or restrictions in screens, pipes, valves or channels for infiltration of undesirable microorganisms.

Long periods of nonuse or occasional use allow fouling growths to build up. Overuse may draw in poor quality ground water or aggravate clogging build up by encouraging sand or mineral clogging and extra oxidation.

How does biofouling and its control affect water treatment?

filamentous biofilmBacteria, oxidized iron and manganese, sulfur and other slimy products are slow killers of resin beds and many iron/manganese removal and other filtration devices. Biofilms overwhelm and defeat carbon filters -- even "bacteriostatic" types and bactericidal resins. They also attack or plug reverse osmosis membranes and cartridge filters.

Aeration-type or redox-media, the backwashable iron filters, tolerate biofouling pretty well, and these make good screening filters for most water systems, small or large. They have to be designed and maintained well, taking the biofouling in consideration - including making sure the backwash is effective in removing most of the accumulated iron debris in the filter bed periodically. Staged cartridge filters (such as 30-micron followed by 5-micron) keep filamentous biofilm out, but expect to replace them every few weeks in some cases.

How is contamination limited during drilling and pump service?

Despite the fact that the most likely source of a microbial population in a well is the aquifer around it, drillers and pump contractors are widely accused of transporting the bacteria about. Drilling and well service cannot be sterile, but some steps are available to minimize the possibility of such transport. Any individual following the steps listed here should be credited with doing all that is feasible to avoid contamination.

(1) Become familiar with local problem wells. A contractor or local official interested in ground water microbial problems such as iron biofouling should make notes on the following on a geologic, topographic, or water resources map:

Areas, wells, or wellfields that seem to have more than the usual number of problems with biological well clogging, corrosion, or water quality. Note "why" if you know.

Unsealed abandoned wells (any lonely windmill in a field), plus landfills, and other sources of potential contamination.

Vulnerable aquifer areas likely to have contact with the surface and allow ready transport of microorganisms. These aquifers should be considered to have biofouling microflora throughout and possibly to be at risk for contamination.

Areas with carbonate or fractured crystalline rock or highly productive sands and gravels.

Shallow aquifers are especially likely to be laced with high microbial populations.

Confined aquifer rock containing gypsum or hydrocarbons, including oil and gas areas, often have problems with bacterially produced sulfides (rotten-egg smell) or slime-forming sulfide-oxidizing bacteria (abbreviated appropriately, SOBs).

(2) Minimize practices that introduce or harbor bacteria during drilling, jetting development, and hydrofracturing. Repeat: Drilling and well completion are NOT sterile pursuits and never will be. Like anything else in the environment, the rig, tools, etc. are covered with bacteria, even when clean.

Drillers can minimize drilling damage impacts and make chlorination more effective at the end by controlling their drilling fluid programs and using lightly chlorinated clean well water or municipal water for fluid mixing, mist, or make-up water. As a customer, you can expect this from your contractors, and feel free to clarify such points with them.

Any jetting development or hydrofracturing should use chlorinated, tested water.

Never introduce untreated, unfiltered creek or pond water into the subsurface or water tank, or use it in any way in the drilling process. Not even if you chlorinate it. Never! Driller readers: Please swear (or affirm) that you will never put surface water into ground water while drilling. THANKS.

Well customers: Taking extra care will cost more initially, but saves in the long run. You don't want a well contractor willing to cut corners on construction quality, sanitation or development just to cut costs – DO YOU? They may reluctantly do so to win your job. Don't ask them to cut corners.

Well contractors: Test the water source and your water-carrying tanks regularly for total coliform bacteria (using state- or federally-approved MUG tube methods such as Colilert or certified labs), and iron and sulfate-reducing bacteria using available test kits, such as BART or MAGs (see following).

Do not use products such as organic polymer drilling “mud” or phosphorus-containing mud breakers. If you MUST use organic polymer muds (there is a gun held to your head? The only product at your remote location in Rwanda?), use extreme care in using and breaking and developing out polymers or phosphates used as mud breakers, both of which are bacterial food (follow instructions, and leave NO residual). Better: Specify and use acrylamide polymers for these purposes.

(3) Develop thoroughly after drilling and always chlorinate after development or after pump service. Well development removes drilling damage and mud that hide microorganisms, and also provides more effective well intake area to minimize the effects of biological buildup when it happens. This takes time, and you may need to explain the benefit to the customer.

(4) Always chlorinate after development or pump service to your state's recommendations (usually 50-100 ppm or so) to minimize contamination due to drilling and service activity. Drillers and pump installers should tell customers they will do this and why, and have them plan for a 24-hr wait if possible before using the water for potable purposes. If they won't wait, well contractors should have customers sign a waiver of responsibility. We recommend that you use sodium hypochlorite (the kind meant for water treatment) if possible, or premix calcium hypochlorite at the surface. Add enough vinegar or dilute (5 %) glycolic acid (NOT HCl) to the chlorine solution to drop pH to about 6, which optimizes hypochlorous acid, which is the lethal hypochlorite ion. Commercial buffers are available for this purpose and should be considered. Note existing ANSI/AWWA and ANSI/NGWA 01 standard practices, your jurisdiction's rules, and other guidance.

(5) Keep tools as clean as possible. After well development or redevelopment, drillers should clean tools thoroughly (to the clean steel). Keep casing, riser pipe, pumps, etc. off the ground and out of the mud. Never reinstall any pipe with any incrustation, mud, or film of any kind without thorough cleaning and chlorination. Chlorinate tools used in redevelopment before going to the next job.

(6) Insist that the customer get proper water analyses run. The well owner or developer should run tests for total coliform bacteria and chemical parameters useful to both health and safety and general water quality (nitrates, hardness, iron, etc.). Proper sampling is crucial. The water should be run long enough to establish aquifer conditions before taking samples.

If sulfur or iron bacteria are a possible problem, tests can be run to analyze these as well. BART or MAG tubes are good for these early analyses. These are now part of Standard Methods Section 9240. Your county or state health laboratory provides or recommends laboratories that provide reasonable-cost coliform tests. We routinely conduct these biofouling analyses and provide recommendations. Contact us for more information.

When is the best time to clean up a biofouling problem such as iron bacteria?

The best time, obviously, is as early as possible before real damage occurs and treatment methods are most effective. This is usually long before noticeable plugging, loss of efficiency, and other gross symptoms become noticeable. The key to catching a growth before it causes problems is preventive monitoring, starting when the well is new or at any favorable point. This advice is also for private water and monitoring wells!

Usually, such a problem will require redevelopment with a well rig, and not just casual shock chlorination. This is work for an experienced well contractor.

What is preventive maintenance monitoring?

While testing will not prevent bacterial contamination or biofouling, it is good to do regular testing for signs of: (1) contamination and (2) the beginning stages of biofouling.

Coliform testing as an indication of contamination is a pretty familiar procedure, but methods also exist that can be cost-effectively employed to detect biofouling in its early stages when it most treatable, instead of later when it is not. Since there is no regulatory enforcement, it is up to well operators with foresight to put this type of monitoring in place. This can be done in cooperation with knowledgeable well contractors, health officials and consultants.

(1) The total coliform (TC) test that is usually mandated as a standard of "safe" water supply is a place to start. It is used to detect indicators of possible surface contact and therefore potential contamination. If the test is not run regularly, the time to start is now. You with the private well: yes you, too. The TC test will not detect the large majority of biofouling organisms or even most bacteria in a well.

Note 1: It is not uncommon for wells showing no coliforms to have very large bacterial populations. Note 2: Some "native" bacteria will cause a "positive" coliform reaction, but take any positive as a reason to look for possible problems.

(2) The heterotrophic plate count (HPC) test is capable of detecting most viable, culturable bacteria (those capable of growth on the test media used) in a water well sample and telling you roughly how many viable, culturable bacteria are present in the sample (which may be very different from the well water as a whole). There is no standard concentration of HPC for concern, but a count of more than 200 CFU/ml is probably an action level. If non-coliform contamination, such as Pseudomonas bacteria, is suspected, HPC is a place to start.

(3) BART or MAG tubes provide a means of detecting heterotrophic (organic carbon-using) microorganisms including those that precipitate iron and reduce sulfur to sulfide, among other types. These are handy and easy to use, but take experience to interpret properly. They have a definite place in a regular quality assurance program for drilling water quality.

A real problem is in the sampling. Nearly all bacteria in a well or aquifer are attached to surfaces and don't come loose easily. For coliform testing, follow recommended procedures and be aware that it is very easy to contaminate a water sample. Pumped sampling is OK for coliform, HPC, or BART or MAG biofouling tests, but usually inadequate to get visible samples of "iron bacteria" for the microscope. Collector surfaces in the well or water stream designed to be withdrawn regularly and examined and tested provide good samples. Effective preventive monitoring for iron bacteria in a well and water system would include both types of testing.

(4) Chemical analyses shouldn't be overlooked. Although iron and manganese are important in plugging, several other parameters are also important, including pH, Eh (redox potential), TOC (total organic carbon), total phosphorus, and nitrogen (as ammonia-N, nitrate-N, and organic-N). Conductivity, total dissolved solids, etc. can be measured or calculated to determine the severity of potential mineral corrosion and incrustation. Other important parameters are sulfates and sulfides and particulates.

(5) On highly valuable or troublesome wells, borehole TV surveys are useful in looking for well construction faults or failure, locating water producing zones, and watching biofilm buildup and corrosion in the well.

(6) When should you test? Tests for TC, biofouling bacteria (using BARTs or MAGs) and key chemical indicators (total and ferric Fe) should be run soon after a well is drilled or serviced in any way, and also at regular intervals, usually annually or at any noticeable change. Tests are an important part of routine maintenance and health monitoring.

If we've got bacterial problems, then what?

(1) If caught early, regular treatment using chlorination (coliform contamination) or chelating organic acids (iron biofouling) and stepped-up vigilance can keep bacterial problems under control. For any treatment, do before and after analyses to judge the effect of the treatment.

(2) In light cases of biofouling, or transient coliform contamination, shock chlorination works. Recirculating chlorine with a hose is enough to mix the chlorine throughout the well to achieve a good exposure throughout the well bore. Adjust the chlorine load to 50 mg/L lethal residual dose (measuring the residual is more sure than calculating a dose), acidified with vinegar (or acetic or glycolic) to pH 5.5-6.5. Test the return flow in the circulating hose. Pool chlorine test kits are sufficient for measuring residual and pH test strips for pH.

Caution: Some water treatment resins are sensitive to chlorination, and care should be exercised in running doses through the bed if a chlorine-tolerant material is not available. Consult local water treatment professionals, the manufacturers of the equipment or reputable consultants in water treatment.

Caution: Chlorine and other chemical solutions are STRONG OXIDANTS and can cause irritation and burns to people, other animals and plants, and damage clothing. Do NOT dump untreated chlorine solutions on the ground or into water ways (that includes storm drains).

(3) In more entrenched cases, such as established iron biofouling, physical agitation such as surging and the use of chelating agents and acids are necessary. Both the chlorinating procedure and more involved procedures you choose will depend a lot on the problem you have, water chemistry, the well itself, etc. Experienced well rehabilitators in your area can help you design a "cure". Knowledgeable consultants (yeah, you guessed it – like us) can help well operators sort out conflicting claims and advice.

Repeat: (1) Chemicals, hot water, and surging can be dangerous. This work is best done by professionals. (2) No known procedure completely eradicates bacteria and their problems.

(4) After any cleaning job, pump until clear, chlorinate and allow to stand 24 hours. Pump the treatment chemicals away or circulate clear, chlorinated water through the water system (careful of softeners and other chlorine-sensitive equipment).

Filters ahead of the water system are helpful in trapping debris kicked up by the well after cleaning. Watch the pump when pumping off water with a lot of solids: well pumps can plug and burn up, and jets always plug. If the pump chokes down and draws excessive amps, shut it down right away, and remove the submerged portions to disassemble and clean. If you can, use a pump specifically for this purpose - preferably one that can be taken down and sterilized between jobs.

Never dispose of unspent acids and chlorine in a septic or aerobic tank, or in any sensitive surface water body. Neutralize at the wellhead (not in the well). There are laws governing even small discharges of chemicals: know and obey them, and be considerate of the neighbors and other wildlife.

(5) Monitor to head off a comeback.

Recurrence of excessive coliforms after treatment is a sign that there is a pathway from a contamination source to the well that must be repaired if possible, the well decommissioned, or continuous chlorination installed as a last resort.

Iron bacteria and other forms of biofouling always grow back - the trick is to get them as early as possible. If regrowth persists, look into regular treatment. A maintenance contract between a knowledgeable well service contractor and the well owner is a good idea.

Note: This paper is intended as a general guide, so the advice herein is general in nature, and may not apply to every situation. If you have questions, we are glad to help. Please contact us - we're happy to answer some questions, and also provide on-site testing, troubleshooting, and consultation services: designing biofouling testing plans or maintenance plans, writing specifications, or evaluating proposals. Other related reports are available from Ground Water Science.


TEXT REFERENCES (Check these out yourself. We can provide publisher references):

  • Standard Methods for the Examination of Water and Wastewater (Available from local sources such as public water supply labs or technical libraries). Now online (where you can also order the hard copy).
  • Ground Water and Wells (Available from NGWA). 1986 and 2007. For general screened water well reference and well development. The well rehabilitation information in the 1986 edition is dated and don't have recent commercially driven information. The 2007 edition is heavy on Johnson's view of well chemistry, and, well... ask us first.
  • Methods for Monitoring Iron and Manganese Bacteria in Water Supply Wells, Research Foundation report by Stuart Smith, from AWWA. 1992. Experience with and recommendations for maintenance monitoring. Now out of print. An updated document that is similar is available from Ground Water Science. Ask.
  • Evaluation and Restoration of Water Supply Wells, Research Foundation report, 1993, by M.A. Borch, S.A. Smith, and L.N. Noble, from AWWA. The out-of-print well M&R encyclopedia. Superseded by Sustainable Wells and our manuals (see following).
  • Tuhela, L., S.A. Smith, and O.H. Tuovinen. 1993. Microbiological analysis of iron-related biofouling in water wells and a flow-cell apparatus for field and laboratory investigations. Ground Water 31(6):982-988.
  • Practical Groundwater Microbiology, Lewis Publishers, Boca Raton, FL, 2008, 2nd ed replacing the 1993 ed., by D.R. Cullimore. This is the handbook on the use of BART biofouling detection tests.
  • Gariboglio, M.A. and S.A. Smith. 1993. Corrosión e encrustación microbiológia en sistemas de captación y conducción de agua: aspectos teóricos y aplicados. Consejo Federal de Inversiones, Argentina. Alas, this work is out of print and we are out of copies. Use of MAG tests (English available). The late and sadly missed Dr. Gariboglio, was among the most experienced biofouling experts in South America. His legacy continues with Laboratorio MAG , which also has its own biofouling tests.
  • Fouling and Corrosion of Groundwater Wells. 1994. National Centre for Groundwater Management, University of Technology, P.O. Box 123, Broadway, NSW.
  • Monitoring and Remediation Wells: Problem Prevention, Maintenance and Rehabilitation. 1995. CRC Lewis Publishers, Boca Raton, FL, by Stuart Smith. You can order that here through our web site.
  • Wellfield Operations and Maintenance Water Quality Testing Manual. 2012. Our own recommendations on the subject. You can order that here through our web site. Updated occasionally.
  • Well Performance Testing and Maintenance Reference Manual. 2012. Our own reference manual for practical every day use. You can order that here from the web site. Updated occasionally.
  • Monitoring, Maintenance, and Rehabilitation of Water Supply Boreholes. Report 137. 1995. Construction Industry Research & Information Assn., London, U.K.

In memory of Miguel Gariboglio, Argentine innovator and pioneer in biofouling monitoring.

Miguel Gariboglio and Stuart Smith 1994 La Plata
Miguel Gariboglio and Stuart Smith 1994 La Plata

This page is dedicated to the late Dr. Gariboglio, who did good work with integrity under difficult circumstances. He and Stuart Smith corresponded from 1981 until his untimely death - through the military government period, 10,000-percent inflation, the Malvinas (Falklands) War, the restoration of democracy, ups and downs in business. A fine man in all respects.

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Tip of the Day

Effective control of the recharge area helps to assure that harmful contaminants do not enter the well, especially for wellfields with little protection from surface contamination.