Biofouling is, in some ways, a very new phenomenon and yet it has existed throughout time as natural events. The fact that these events can often occur naturally leads people to accept the effects as a "normal" act of nature and a part of the normal risks that have to be accepted. Biofouling is however a complex event and each event is, in some senses, unique. While the effects (or symptoms) may be definable, the cause may be complex and difficult to determine. As J.H. Woodger wrote in "Biological Principles" published by Routledge and Kegan Paul, London in 1929, this was summarised by the statement that: "All the wood stands in a mist of green and nothing perfect". For biofouling even the "mist" remains difficult to see and "nothing" can ever be perfect!?

Frequently, biofouling events have been considered to be primarily physical and/or chemical events because the effects were often readily interpretable by those techniques. For example, a loss in flow from a well was simply a result of silting or encrustation (ie, physical blockage and chemical clogging). The corrosion of a iron pipe may be considered to be simply an electrolytic corrosion event which is primarily physical in form. With the advent of improved microbiological methodologies and a growing need to extend the life expectancies of installations for environmental and economic reasons, there is a rapidly growing awareness that biofouling can no longer be treated as simply a necessary but unpredictable risk, but that it is definable, controllable and can allow extensions to the useful lifespan of an installation.

This section essentially with the "cause and effect" of biofouling backwards. This is being done because very often it is the symptoms of biofouling (ie, effects) which become evident and set in motion a rehabilitation and (hopefully) a preventative maintenance program to control the problem. The "cause" of biofouling will be approached later in this section once the various effects have been defined.

Clog can be defined as "an encumbrance or impediment" while clogging may be considered to be "become obstructed, esp. by accumulation of a glutinous mass". This definition covers many of the primary aspects of clogging in a biofouled water well. First, there is a glutinous mass which could related to the formation of a slime from coalescent biofilms. Second, there is an encumbrance, impediment (to flow) which is caused as the clog fills the void spaces in the porous media and reduces water flow. Third, there is an accumulation of material within the clog indicating that it is growing and therefore likely to become more obstructive. Clearly from the brief definition many aspects of the growth can be projected. There are two major features of concern: accumulation and obstruction.
A clog can be considered to be comprised of four parts which dominate at different times in the growth cycle. These are:
1. The living microbial cells which form the "heart" of the clog although they may not occupy a very large part of the volume.
 2. The EPS which forms a part of the volume of the clog. It forms the glutinous mass and holds "bound" water along with other accumulates.
 3. Amorphous chemical complexes which may be formed within, or attached to, the clog.
4. Crystalline chemical complexes which may be formed directly or via the amorphous forms. Crystalline complexes often arise at interfaces between the clog and either solid surfaces, the free flowing water or the atmosphere. The chemicals may be dominated by particular carbonate, oxide or hydroxide salts.

The mechanism of growth causes a range of effects which relate to the relative state of the clog. During the growth of a clog, the above parts change in their ratio of one to the other.

The Relative Shifts in Dominance during Clog Formation

               1              2              3              4
          Viable cells   EPS slime      Amorphous      crystalline

Attachment     +++            +              -              -
Early growth    +            +++             -              -
Stabilization   +             ++             +              -
Cyclic growth   +             ++             ++             +
Encrustation    +             +              ++             +++
Occlusion       +             ++             +++            ++
As the clog forms it goes through a number of stages of maturation (see table above). Initially there has to be attachment of microorganisms to the surfaces within the porous medium or non-porous materials. This attachment is achieved by the viable cells "throwing down" EPS to anchor the cells to the surfaces. Early growth involves the attached (sessile) microbes now producing copious EPS which occupies a very considerable amount of the void volume if porous media are being infested. The net effect of this is that there is a loss in porosity and the water flow may be severely impaired. This is a temporary phenomenon which is sometimes seen to influence the initial production from new wells before they have been "developed". Very rapidly, the initial slime formation condenses and stabilizes with a residual very thin growth remaining over the infested surfaces. Flows now return and stabilize. In laboratory microcosms, the flow from a newly stabilised clog formation can exceed even the flow from through the porous medium in the pristine (unfouled) state. There now begins a period of cyclic growth in which there is a pulse-like increase in the volume of the clog as it occupies more and more of the void space. From the laboratory and some field experiences, the pattern always appears to follow the same pattern: (1) expansion of the volume; (2) sloughing; and (3) stabilization. In production wells, this pulsing may be seen by regular shifting in the draw-down of the well depending upon the point in the life cycle that the clog is in. During this cycle there is a gradual increase in both the amorphous and crystalline forms occurring within and around the clog. A process of bioaccumulation of recalcitrant chemicals is underway which means that there is a shift in the dominant components away from the cells (1) and the EPS (2) towards the amorphous (3) and the crystalline (4) components. Both the amorphous and crystalline deposits are essentially recalcitrant in that the residual microbial population may not be able to utilize these chemicals for any purpose. However, the energetics of the system remains to be established.

When encrustation are produced, these may be dominated by crystalline form of carbonate and oxides. The surfaces become smooth and hardened and the microbial population and EPS content shrinks very considerably. Generally, an established stable encrustation does not radically affect flow or water quality to a variable extent. Any changes that do occur are relatively slow in appearing. When occlusion of the void spaces occurs, there still be a significant microbial population with a significant EPS present. Much of the chemicals may remain in the amorphous form but the occlusion can cause total loss in flow through the infested porous media.

Clog formation may therefore have a number of sequential impacts on the water being drawn from the wells as a result of the different stages in the clog formation. The symptoms will change with the age of the clogging and the rate at which it is generating.

Chronological Sequence of Symptoms in Clog Formation
Short unstable period of production as the clog goes through the early stages of growth. This is associated with the high (but short lived) void volume occupancy which occurs during early colonization.

Good production of water at capacity with the product water being of a higher quality than the groundwater feeding the well. This is because the biological interface being established as a part of the clog around the well is removing nutrients and various metals (eg, iron, manganese, zinc, aluminium, copper etc.) from the water as it moves across the redox front. The nutrients are utilised by the clog formation for growth while the metals and other recalcitrant material bioaccumulate.

Water production becomes variable. The draw down against a stable pump rate may vary on a day-to-day basis and reflects the status of biofilms within the clog as they pass through growth, slough and stabilisation phases. Water quality may become more variable; declining during the sloughing, and recovering and stabilising during the other phases. This variability in the water quality sometimes creates an attitude of uncertainty in the interpretation of the data obtained.

There now develops a general but erratic loss in both water production rates and the quality of the water. Frequently, the TSS in the water increases along with color. This is a reflection of the radical but often random sloughing of the clog formations. These symptoms are the result of an increasing amount of sloughed particulates which still retain the bioaccumulates. Some of these accumulates may also be present and dissolve (and color) into the water itself. Water production is affected by the reduction of porosity created by the clog now filling a significant percentage (usually >40%) of the void volume. This may be reflected in increasing draw-down within the well and an increased probability of over pumping causing the draw-down to cause the pump to "suck-air".

The terminal state is reached when the production capacity of the well is so impaired that it is not practicable to rely on the well as a source of water. The clog has essentially occluded (plugged up) the formation and is acting as an unstable structure. Such instability leads to the product water quality degenerating still further and becoming unacceptable even if the flows were adequate. Such wells now require radical rehabilitation in order to disperse the clog and return the well to an acceptable production. Failure to rehabilitate the well for economic or other considerations leads to the abandonment of the facility.

There are reports of abandoned clogged water wells returning to an acceptable production after they have been left essentially untended for a period of years. These "spontaneous" recoveries from clogging may be a reflection of the changing environment which occurs in and around the well after it has been abandoned. The well reverts to become simply a biofouled part of the groundwater system. As a result, the environmental characteristics of the habitat around the well changes as the redox from either dissipates or moves. In either event, the microorganisms still occupying the clog formation will tend to migrate towards a more acceptable environment (eg., another redox front somewhere else). This act of migration can destabilise the clog structure and cause a gradual dispersal of the elements concentrated within the clog. Over time such traumatised clogs may become dispersed completely so that the well can, at least theoretically, be brought back into production after suitable rehabilitation.

As the cost of operating water wells increases for various reasons, this option of rehabilitating even totally clogged installations becomes a more tempting option which is only now beginning to be appreciated. Various techniques discussed in later chapters can be applied to such "last resort" rehabilitations.

Clog formations involve a system of bioaccumulation which may be active (microorganisms utilize some element of the accumulation for a specific purpose) or passive (the deposition is purely a physical and/or chemical event which does not involve any microbial activity). The chemical accumulates fall under two general headings: amorphous and crystalline. Amorphous deposits have an indefinite shape and structure while crystalline deposits usually have a more defined structure and edges sometimes with evident internal structures. These accumulates are recalcitrant (not immediately utilisable by the microbes within the clog) but may eventually become modified (eg, to a different from or dissolved) by subsequent action which may or may not involve microbial agents.

There is a very limited knowledge of the role of microorganisms in the precise mechanisms involved in bioaccumulation. Of the crystalline deposits, carbonates, oxides, hydroxides and oxyhydroxides may dominate. Calcite (CaCO3) may be a major carbonate along with some siderite (FeCO3) where iron is being bioaccumulated. Other iron compounds that may be present include hematite (Fe2O3), and geothite (FeO(OH)). Noncrystalline (amorphous) minerals commonly found may include ferrihydrite (Fe5HO8.4H2O). Both crystalline and amorphous forms of chemicals are often complex involving a range of substances involving other elements and complexes.

The nature of the chemistry of these events is that each clog formation may have a unique composition and thus will have a different nature in its growth and control. As more is discovered about the nature of clog formation a better understanding should be generated as to their control.

Another factor affecting the characterization of a clog is the fact that the chemicals being accumulated do not do so in a random manner. There is an awareness that the cations (eg, metal ions) accumulate in a sequence as the water flows over the clog. Wells in which the clog has been dispersed and surged out of the well sometimes exhibit changes in the ratios of the metallic elements as the dispersed clog is being pumped from the well. Iron for example tends to accumulate on the oxidative side of the redox front and is therefore much of the bulk is removed early in the pumping procedure. Manganese, on the other hand, tends to accumulate deeper into the clog formation under more reductive conditions. This differentiation into different sites of accumulation may relate to the polarizability, number of outer shell electrons, and the degree of symmetry in the cation. Where organic compounds are involved in the accumulation process, there may be a form of bonding between the metal and the ligand (organic site of the bonding). There are two mechanisms in which this bonding can occur. First, the bond may be formed as ion pairs in which both the metal and the ligand retain hydration (bound water) sphere. Second, a coordination complex may form in which the ligand is immediately adjacent to the metal and some degree of electron donation occurs between the metal and the ligand. Sometimes these complexes can involve multiple ligands and form a chelate complex.

The nature of these very complex structures renders any control strategy that much more challenging to implement. Not only that, the effect of dispersing and pumping out a clog formation means that the product flow will contain the various chemicals accumulated within the clog. One irony of this is that the clog may have for a number of years been "filtering" the groundwater to provide a better product water, but is then dispersed and now yields the bulk of the "filtered" material and may now be considered under some circumstances to be a hazardous waste.

In general the water quality for a given well is established after the well has been "developed" and gone into service. This act of development is a period during which the well stabilises. Stabilization may also be viewed as occurring at the beginning of the third phase of the biofouling after compression of the clog. Compromise occurs as the water quality begins to degenerate as the clog matures. Symptoms will vary from well to well but the general features that may be expected are listed below by parameter.

Iron, there is a phasic effect in which there would be initially an erratic rise in the amount of soluble iron in the water which may color the water to a yellow or orange hue. However there may not be any significant increase in turbidity. This would be because much of the iron may be retained within small biocolloidal particles which would not influence the turbidity so much. There may be some variability in the total iron recorded and this would reflect the stability in the clog formation (eg, the degree of surface sloughing occurring. Repeat samples over a period of a few days may show significant differences between each other since the clog may be in a stable - unstable cycle within the maturation period.

As the clog continues to mature, the sloughing events may become magnified leading to the secondary symptoms. These include a degenerating increase in turbidity, higher total iron content, larger particles and a high TSS. This may often be accompanied by significant (>15%) drops in the production capacity of the well due to occlusion. As this happens there may be a very significant precipitation of these particles in the well water column leading to the build up of a sediment which may resuspend when the well becomes active. Very often the early flow from an infested well will be very high in particulate material and iron and should be diverted to waste in order to avoid seriously challenging the downstream systems and processes.

Total Organic Carbon, this is a prime source for the growth of heterotrophic microorganisms since this contains both the source of carbon and often the source of energy for the microorganisms. Because of this, the TOC in the water may be lowered as it passes through the clog formations around the well. In laboratory microcosms it is not uncommon to find greater than 85% of the TOC becoming bound within biofilms (and therefore removed from the water). Generally TOC values will remain low until there is a destabilization and massive sloughing from the clog formations. When this happens, the TOC values may become elevated by as much as an order of magnitude. These elevations may be unstable and be a reflection of the degree of sloughing that is occurring along with any resuspension of materials that have precipitated in the bore hole and other "dead" ends within the system. TOC in the product water cannot by itself be used to diagnose the likelihood of a biofouling event and usually reflects the occurrence of such an event after there have been other, and often more obvious, symptoms.

Total nitrogen. Nitrogen is very often not estimated in water wells beyond nitrate which forms a hygiene-risk to infants when the concentration exceeds 10 ppm. The form in which the nitrogen occurs in the water can be used to project with some accuracy the form of biological action that is occurring in the upstream biological interfaces. Nitrogen is commonly estimated using the following parameters:
     N3   Nitrate nitrogen    -    N - NO3
     N2   Nitrite nitrogen    -    N - NO2
     NH   Ammonium nitrogen   -    N - NH4
     NO   Kjeldahl nitrogen   -    ON   -    organic nitrogen + NH4
The ratio for these different forms of nitrogen can give an indication of the status of the biological systems in the upstream interfaces. Given that the total nitrogen (TN) is:

TN = NO + N3 + N2

A number of extrapolations can be made and these are addressed below.

>0.2 = NH/NO

There is a significant amount of ammonium relative to the total Kjeldahl nitrogen which would suggest that the water contains unoxidised (anaerobic) degradation products and any clog formation may be dispersed in form since no redox front has become established.

>0.4 = N3/NO

Nitrification is likely to have been occurring extensively upstream in an oxidative environment possibly through a shallow aerobic polluted recharge. Frequently such pollutants may be relatable to sewerage or septic tank wastes which are degrading aerobically. The nitrate concentration may be transient (and variable) since many microorganisms are able to use nitrate as an alternate respiratory agent to oxygen.
>0.6 = N2/N3

Denitrification is occurring in which the nitrates are now (anaerobically) being reduced via nitrite to nitrogen (complete denitrification). When this is occurring, usually on the reductive side of the redox front, the nitrate concentration may be variable and generally decline as the denitrification continues.

>0.8 = NO/(N3 + N2 + NH)

The amount of organic nitrogen exceeds considerably the sum of the inorganic nitrogen which would imply that a sloughing (or growth) is dominating the nitrogen mass balance in the water. Active biofouling (such as clog formation) may be suspected to be present upstream in this event.

Total Phosphorus, phosphorus in biological systems is akin to the battery in an automobile. It provides the energy storage system (as ADP and ATP) which drives the biological systems. It is therefore a very essential and sought after element (rather similar to the human desire for gold, biological systems desire phosphorus. The net effect of this essential need is that phosphorus is "hoarded" by biological systems and may not, therefore, be as readily released into the water in the soluble form. In the cell, phosphorus may occur as orthophosphate (the currency), polyphosphate (the reserve) and metabolic phosphorus (the energy driver). In water, phosphorus is normally found in four states:
     SIP       Soluble Inorganic Phosphorus 
     PIP       Particulate Inorganic Phosphorus
     POP       Particulate Organic Phosphorus
     SOP       Soluble Organic Phosphorus
which together form the total phosphorus (TP). The ratios of these fractions of the phosphorus pool can be used to diagnose some biofouling problems.

>0.3 = SIP/TP

A dysfunctional system in which there is some level of trauma for whatever reason which is allowing the SIP (usually as orthophosphate) to pass through the upstream environment without being taken up by the biological interfaces. The trauma may be created by some radical shift in the conditions resulting from such events as a disinfection treatment or a sudden and dramatic change in the environmental conditions.
>0.5 = PIP/TP

Much of the phosphorus may be in a recalcitrant form not readily utilisable by the upstream biological interfaces. Such phosphorus may not necessarily be relatable to the amount of biofouling that can be expected. It should be remembered that this ratio may be distorted upwards by the retention of the other forms of phosphorus (SIP, SOP and POP) within the zone(s) of biofouling.

>0.2 = SOP/POP

An inordinately high SOP to POP ratio would indicate that there was either a disintegration of the biological interface with the releases of SOP from the cells which constitute the POP. This could happen where there has been a successful dispersement of a clog (for example).

>0.85 = POP/TP

Much of the phosphorus is probably bound within biocolloids and other particles. Much of this phosphorus may be in the form of reserve polyphosphates and the organisms within the particulate mass are probably still viable and have not been disrupted.

An idealised ratio for the SIP:PIP:POP:SOP in a very active planktonic system may be expected to be in the range of 0.1 - 0.2 : <0.05 : >0.8 : <0.1 respectively. However, in a groundwater situation, the "site of growth (eutrophication)" may be some distance from the sampling point and so the ratio in the sampled water will, most likely, be distorted away from the optimal towards that generated by the sloughed and recalcitrant chemicals passaging through the system.

Phosphorus is commonly perceived as the major nutrient limiting growth. One of the reasons for this is that the phosphorus is such a desirable (and storable) nutrient. Very often analyses of product waters reveal very low levels of phosphorus and the natural conclusion is that phosphorus must therefore be the limiting nutrient for growth. In reality much of the phosphorus could be tied up by the biomass (concentrated at the redox fringe) as polyphosphates. To truly determine the clogging potential, the mass balance for phosphorus within the likely zone of clogging would need to be determined.

Redox potential, it has already been stated that the biological (and relatable clogging) activity will focus at the redox front as the water moves from a reductive to an oxidative state. Product water is commonly sampled from the oxidative side of the redox front and may therefore not be very useful in determining the position of the front itself. However, if there is a low redox value (eg, 0.05 - 0.00 millivolts) then the biofouling is probably close to the sampling site. A negative redox value (-0.00 - -0.20 millivolts) may indicate that the major biofouling could occur downstream from the sampling point.

Temperature, it has now generally been believed that a temperature gradient can be created in a well which is actively undergoing a biofouling. Recent studies have revealed that minor gradients can be created which are measurable and do focus on the sites of biofouling. Generally, the temperatures found in most water wells fall within that broad band of temperatures (6 to 40oC) where a wide spectrum of biological activity is potentially able to be active.

Microbiological, the irony of determining the presence of microorganisms within a product water is that most of the biological activity will be at the clog formation and other sites related to the redox front. These activities will be dominated by attached (sessile) microbes growing within the fouled zone itself. Consequently, the product may contain vary anomalous (commonly low) presences of microorganisms compared to the true amount of activity that is occurring. Historically these observations, together with the absence of coliform bacteria, has led to an underestimation of the role microorganisms in the fouling / clog formation processes. Essentially, there has been a mixture of denial and ignorance which has downplayed the role of microbial aggression in the clogging and fouling of wells.

Given that the water is commonly sampled from the well water column or downstream, the water quality has already been compromised by the upstream biofouling, the product water quality and flow may degenerate very slowly if the production demands are close to the wells designed capacity. If the well is being operated below capacity then the impairment of flow by clogging may be a relatively dramatic event.

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