Vaccari D.A., Strom P.F., Alleman J.E. Environmental Biology for Engineers and Scientists

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ants that ‘‘herd’’ so-called ‘‘ant-cattle’’ stocks of aphid and larvae life-forms. One such

exemplary leaf-cutting ant group may be found in Central and South American regions

(e.g., typically associated with the Atta genus), where individual chambers within their

colonies are allocated to carefully managed farming operatio ns. These particular ants nur-

ture, and then feed exclusively from, a form of fungus found only within these unique

subterranean systems. Leaf and grass cuttings gathered by ants on the surface are carried

underground to nurture the fungus growths held in chambers inside the colony, even to the

point of using protease-rich anal secretions to ‘‘fertilize’’ the cuttings. Multiple fungal

growths are raised on staggered 3- to 4-week cycles, with the ants living off the cloned,

reproductive fruiting buds that grow on the fungus surface.

Whether their mode of sustenance were that of farming, herding, or just grazing, how-

ever, ant cultures have also adopted remarkably advanced measures for applied waste

management. Ants routinely remove residues generated by farming or herding, along

with dead members of the colony and other debris, to remote dumping sites located either

deep within the underground colony or on external surface spoil sites carefully chosen to

provide a downhill, easy-discharge location. Furthermore, most ants exhibit a fastid ious

disdain for contact with their wastes and garbage, and in some colonies there are even

special ant groupings solely assigned the task of policing waste.

At least when measured within a historical timeframe, ants appear to have far sur-

passed humans in terms of waste management concerns, extending back millions of

years instead of a few centuries. In our own case, large-scale organized efforts to collect

and remove wastes were not implemented until after the Industrial Revolution, roughly

three centuries ago, and controlled use of biological waste treatment as an environmental

management tool extends back barely half that time.

Of course, although humans may have been beaten by ants on a time scale, we have

now advanced the sophistication of our applied biology efforts to a far higher level, and

this book’s environmental management theme certainly demonstrates this progress.

Whereas ants have long been content with just collecting and discarding wastes, human-

kind’s modern approach to environmental engineering and science has developed and

adopted far more advanced measures.

Developing an appreciation for, and understanding of, the biological processes now

used for treatment of contaminated air, water, soil or solid wastes involves the basic prin-

ciples of biology that we discussed earlier. Basic biology, especially biochemistry, gov-

erns all the processes involved. Microbiology is critical, since microorganisms dominate

these processes, but there are also processes that depend on higher plan ts and even trees to

degrade various wastes and/or to remediate the land on which they live. Finally, an under-

standing of ecology is necessary, since all of these processes involve mixtures of numer-

ous interacting populations of organisms, and in some cases the consortia of organisms

are able to achieve treatment goals that could not have been achieved by individual popu-

lations (Atlas and Bartha, 1987).

In whatever fashion the various mechanisms of applied biology might be used, though,

the resulting beneﬁts of preserving and protecting our natural assets are readily obvious.

Biological systems inherently qualify as environmentally friendly, and as a naturally

renewable resource they tend to offer signiﬁcant economic advantages. At the same

time, backed by eons of evolutionary adaptation, biological mechanisms commonly pro-

vide a highly effective, and metabolically diverse, strategy for effectively transforming

waste residuals into innocuous by-products. Should it be necessary, most of these systems

can even self-adjust (i.e., acclimate) to their circumstances (environmental conditions,

578 BIOLOGICAL APPLICATIONS FOR ENVIRONMENTAL CO NTROL

competitive pressures, etc.), in an attempt to maintain optimal performance while hand-

ling metabolically an increasingly complex array of industrial chemicals, which may be

anthropogenic (human-made) or xenobiotic (foreign to living things).

The following seven sections (Table 16.1) will provide brief introductions to several of

these engineered applications with biology and their associated technical features. In each

case, these summaries explore the backgrounds of the applied technologies and present

overlapping views of the biological and engineering principles involved. Upon reviewing

these sectio ns, and again in keeping with the critical role of microbiology, it will be read-

ily apparent that the major ity of these ‘‘biological’’ mechanisms operate largely at the

‘‘microbi al’’ end of the spectrum of life. Indeed, bacterial biomass commonly represents

the driving force behind the success of most engineered processes, both in terms of the

shear numbers of cells involved and their metabolic contributions.

Granted, there are usually a number of complementary roles played by higher life-

forms in a number of these systems, but the true backbone of these operations typically

hinges on the performance of the bacteria involved. Indeed, even in the case of wetland

and phytoremediation systems, these plant-based processes depend heavily on microbial

(and largely bacterial) mechanisms that operate on the surfaces or in the immediate vici-

nity of their root systems.

Although the following sections were written with heuristic conﬁdence about the pro-

cess of designing and operating these biological systems, a fair and honest acknowledg-

ment of our inherent limits is warranted. Whether wastewater microbes or constructed

wetland plants are to be used, it is rather rare that we can select and sustain the exact

group of organisms that we might feel can best accomplish a desired treatment goal, par-

ticularly when more often than not, these systems are open to the inﬂuence of opportu-

nistic biota living within the natural environment. Instead, we identify desired goals,

establish the environmental conditions involved, and design an appropriately engineered

system, at which point nature will play a signiﬁcant, if not the dominant, role in selecting

TABLE 16.1 Biological Applications for Environmental Control

Biological Level

Applied Realm of Speciﬁc Process

Environmental Management Application Micro-scale

Macro-scale

Wastewater Attached growth 

Suspended growth 

Stabilization lagoons 

Constructed wetlands 

Sludge Anaerobic digestion 

Aerobic digestion 

Composting 

Water Potable water 

Disinfection Water and wastewater 

Solid waste Landﬁll degradation 

Air Bioﬁltration 

Soil and groundwater Phytoremediation 

Bioremediation 

Microscale applications involve various combinations of bacteria, protozoms, rotifers, fungi, algae, etc.

Macroscale applications involve higher plants.

BIOLOGICAL APPLICATIONS FOR ENVIRONMENTAL CONTROL

579

the resulting mix of operative species working within our processes. Even then, however,

the most rewarding aspect of applied environmental biology is that by merging our scien-

tiﬁc and engineering skills with the formative power of natural life forces, we can secure

synergistic outcomes with truly global beneﬁts.

16.1 WASTEWATER TREATMENT

Historically, wastewater processing qualiﬁes as our ﬁrst approach to using applied biology

constructively on an environmental basis. Natural biological processes have, in fact, dealt

with the world’s various waste streams from the earliest days of microbial life eons ago,

but our own efforts with respect to waste management were barely better than those of

ants until well beyond the Renaissance, content as we were with pri mitive privies, latrines,

and pits for mere containment rather than complete treatment (Asimov, 1989).

Remarkably, our initial motivation to use applied waste treatment roughly ﬁve centu-

ries ago was neither that of resolving serious and escalating health concerns tied to disease

transmission nor that of reducing widespread aesthetic degradation. Instead, our original

goal was actually that of commercial manufacturing, whereby our residuals might be

transformed from disagreeable wastes into truly useful products with monetary value.

The classic set of sixteenth-century lithograph prints shown in Figures 16.1 and 16.2

depict two such waste processing systems, located in England and Germany, respectively,

both designed in a fashion that we might presently qualify as biological nitriﬁcation ﬁl-

ters. Urine and other nitrogen-rich wastes (e.g., slaughterhouse efﬂuents) were pumped or

ladled onto the ﬁlters and allowed to trickle over and through the piles. In turn, nitrate-rich

Figure 16.1 Sixteenth-century English nitre farming.

580

BIOLOGICAL APPLICATIONS FOR ENVIRONMENTAL CONTROL

salt crystals (i.e., long know to alchemists as nitre) would then be scraped from these ﬁlter

surfaces and sold as a key ingredient for producing gunpowder.

These commercial operations predated the discovery of bacterial life by several centu-

ries. It was not until the late nineteenth century that we ﬁnally understood the tru e litho-

trophic basis for reliance on biochemical nitriﬁcation to convert reduced ammonia to

oxidized nitrates. Despite this fundamental uncertainty, nitre pile waste processes contin-

ued to represen t a signiﬁcant chemical manufacturing industry for several centuries and

was even used for critical nitrate production during the Civil War by Confederate states in

the southern United States.

Midway through the nineteenth century, a number of larger English cities began to use

a patented processing scheme to recover waste nitrogen, but in this case the desired pro-

duct was a nutrient-rich fertilizer. These so-called ‘‘ABC’’ systems used an altogether

unusual set of chemical additives, including alum, blood, and clay (i.e., hence the unique

acronym) to clot and sorb a wastewater’s unwholesome contaminants while generating a

nitrogen-bearing agricultural fertilizer sold under the promotional trade name ‘‘native

guano.’’

At about the same time, securing complementary environmental beneﬁts with waste-

water treatment began to reach beyond the product-oriented stage, catalyzed both by the

latest discoveries in microbiology and medicine and a belated recognition of the inherent

necessity for sanitary and environmental improvements. These early years in the ﬁeld of

wastewater treatment were exciting times for this ﬂedgling niche of applied environmen-

tal biology.

Land application opera tions were the earliest large-scale systems used for wastewater

treatment, with several such operations being in use in Europe. The ﬁrst land-application

‘‘ﬁlters’’ were remote tracts of land onto which wastewater would be spread, being

cleansed as it passed through the soil. As our understanding of, and appreciation for,

the underlying microbial mechanisms evolved during the middle to late nineteenth cen-

tury, simple in-groun d ﬁlters were soon followed by a steady progression of ever more

Figure 16.2 Sixteenth-century German nitre farming.

WASTEWATER TREATMENT 581

advanced, and more heavily loaded, intermittent soil ﬁlter, contact bed, and trickling ﬁlter

wastewater systems. In each case, the soil, gravel, rock, slate, and slag media surfaces

involved were found to be densely covered with an attached bioﬁlm rich in waste-degrad-

ing biomass, following a wastewater processing mode now classiﬁed as attached-growth

treatment.

Early in the twentieth century, another seminal discovery was made that coagulated

and se ttled biomass suspens ion s s u ch as thos e derived fro m either settled dis ch a rge s

taken from the early attached- growth bioﬁlm reactors or from even newer suspended-

growth (as opposed to attached-growth) biomass tanks, could actually be recycled

back to an aeration chamber for subsequent reuse, thereby accelerating the overall

metabolic efﬁcacy of these biological wastewater processing systems. Largely developed

at Manchester, England, by Sir Gilbert John Fowler in the period 1912–1915, with several

large full-scale facilities being built around the world within a period of just a few years,

this newly devised activated sludge concept rapidly evolved into yet another parallel

mode of suspended-growth system, further escalating the sophistication and effectiveness

of wastewater treatment (Horan, 1 990).

In the twenty-ﬁrst century, the applied science of biological wastewater treatment con-

tinues to evolve in terms of the level of technical sophistication employed. Attached- and

suspended-growth options still comprise the two major options for biological treatment,

but in either case these older technologies have been upgraded in technical complexity

and hardware, including all manner of internal pumping schemes, advanced aerators,

online instrumentation, and computer-based control and automation. Whatever the

approach, these wastewater processing systems now arguably represent the largest con-

trolled application of microbiology in the world, at a scale far outstripping that of com-

mercial and industrial fermentation and pharmaceutical production.

Whether based on attached- or suspended-growth processing methods, the overall tech-

nology of wastewater treatment (i.e., as applied in large-scale fashion by cities and indus-

tries rather than that of small-scale septic tanks, etc.) includes an integrated collection of

processing steps encompassing not only biological processes, but also a complementary

set of physical and chem ical mechanisms. Figure 16.3 depicts the processing steps used

with these types of conventional four-step systems. The initial preliminary treatment

step screens, settles, and separates coarse solids, and a primary treatment step provides

further solids separation, either by ﬂoating or settling. Primary treatment may remove

onehalf to two-thirds of the incoming suspended solids and perhaps half as much of

the biochemical oxygen demand (BOD), but neither preliminary nor primary treatment

is able to remove colloidal or dissolved contaminants.

A subsequent secondary treatment step is used to remove the remaining biodegrad-

able contaminants and suspended solids. As reviewed in the following sections, secondary

treatment is typically completed using one of four typi cal processing options, including

attached-growth (e.g., trickling ﬁlters) and suspended-growth (e.g., activated sludge) sys-

tems, stabilization lagoons, and constructed wetlands.

16.1.1 Process Fundamentals

It is common to view biological treatments basically as biodegradation processes, but this

is only partially true. To a great extent, they are contaminant-separation processes. In the

case of domestic wastewater treatment, they convert colloidal and dissolved solids to a

form that can be removed by gravity sedimenta tion into a concentrated by-product cal led

582 BIOLOGICAL APPLICATIONS FOR ENVIRONMENTAL CO NTROL

sludge or biosolids. They typically yield about 0.5 to 0.7 kg of biosolids (dry weight) per

kilogram of BOD removed. Thus, they convert a large problem (the volume of wastewater

to be treat ed) into a much smaller problem, but one that still needs an ultimate solution.

The dominant biochemical mechanism in the vast majority of secondary wastewater

treatment processes is that of respiration, which is distinctly different from that of the fer-

mentation reactions that come into play more often in the sludge processing systems (e.g.,

anaerobic dige stion) used to process wastewater residuals. Both respiration and fermenta-

tion depend on a balanced set of redox reactions (i.e., coupling oxidation plus reduction

steps), which are li nked, respectively, to electron donor and acceptor compound conver-

sions.

With respiration, both reduced biodegradable organics (i.e., carbonaceous BOD) and

reduced, energy-rich inorganics (e.g., ammonia, nitrite, sulﬁde, ferrous iron) in the raw

wastewater may be oxidized to secure energetic electrons, compounds referred to as elec-

tron donors. Conversely, the electrons will then be ‘‘respired’’ or consumed by an elec-

tron acceptor compound. In most conventional wastewater treatment, dissolved oxygen is

preferred as the electron acceptor, so that the zero-valence gas-phase diatomic oxygen

) species is reduced to water.

From a thermodynamic point of view, oxygen is the most favorable electron acceptor,

and aerobic or facultative cells always opt for this aerobic respiration pathway if sufﬁcient

oxygen (i.e., greater than a few tenths of a milligram per liter) is present, largely ignoring

other electron acceptors that might be available. Even in the absence of oxygen, respira-

tion may be continued, following a pathway referred to as anoxic respiration, using a

variety of alternative electron acceptors, such as nitrate, nitrite, sulfate, and oxidized

iron and manganese. Whether aerobic or anoxic, the fact that respiration relies solely

on inorganic electron acceptors is a notable feature for respiration and a key reason

that fermentation is not used widely for was tewater treatment. Indeed, using anaerobic

Settling

tank

PRELIMINARY

PRIMARY

Biological

Treatment

System

SECONDARY

Preliminary

Wastewater

residuals

processing

and disposal

suspended-growth,-

constructed wetland,

stabilization lagoon)

Settling

tank

Secondary sludge

Primary sludge

Raw wastewater influent

PRELIMINARY

PRIMARY

DISINFECTION

Biological

Treatment

System

SECONDARY

Clean wastewater effluent

discharge to receiving waters

Preliminary residuals

(i.e., grit, rags, etc.)

Wastewater

Treatment

Residuals

(e.g., Attached

constructed wetland,

stabilization lagoon)

Figure 16.3 Conventional wastewater treatment processing scheme.

WASTEWATER TREATMENT 583

reactors rather than aerobic reactors would incu r a far higher level of odor emission in

these plants, brought about by volatile organic emissions generated reduc tively through

fermentation.

Although characterized as biological processes, secon dary treatment systems also

involve a complex array of chemical transformations (e.g., acid–base, redox, chelation,

sorption) and physical transfers (e.g., gas-liquid exchange, heat transfer). Furthermore,

secondary biological operations involve biochemical mechanisms that couple removal

and production pathways. Contaminants are removed via catabolic oxidization and ana-

bolic assimilat ion while producing a concentrated waste product calle d sludge or bioso-

lids, contain ing residual particulate solids at concentrations on the order of 1% or higher

(i.e., 10,000 ppm).

Notwithstanding their mutual reliance on aerobic respiration, there are considerable

differences between the four main options for secondary wastewater processing in

terms of their involved engineering and biological details, and there are also dramatic var-

iations in their necessary footprint areas relative to high vs. low waste loading rates. Of

course, the more heavily loaded, mechanically intensive attached- and suspended-growth

systems would commensurately require the smallest land areas; the more natural slow-rate

and lowly loaded design options (i.e., constructed wetlands and lagoons) would require far

larger land areas. Figure 16.4 compares the typical organic loading rates (i.e., representing

Footprint Surface Area (m

0.001

0.01

0.1

1 10 100 1000 10000 100000

Organic Loading (kg/m -day)

0.1

100

1000

10000

Suspended

Growth

Attached

Growth

Constructed

Wetland

Stabilization

oon

Hydraulic Retention Time (hrs)

Suspended Growth

Attached Growth

Constructed Wetland

Stabilization Lagoon

Footprint Surface Area (m

)

Suspended Growth

Attached Growth

Constructed Wetland

Stabilization Lagoon

Figure 16.4 Comparative engineering features with four alternative 1000-person municipal

wastewater design options.

584

BIOLOGICAL APPLICATIONS FOR ENVIRONMENTAL CONTROL

the daily mass of applied organics per unit volume of tower, tank, wetland, or lagoon) that

might be emp loyed with each such design option, together with an estimate of the land

areas (i.e., footprint) required to process the daily wastewater ﬂow for an imaginary city

of 1000 residents (assuming a daily per capita ﬂow of 400 L and a BOD strength of

150 mg/L). As can be seen, there is a dramatic difference in the footprint size linked

to these four alternatives, based on their varied loadings.

Two parameters can be used to compare wastewater treatment processes: hydraulic

residence time and solids residence time. Hydr aulic residence time (HRT) is the volume

of the process divided by the ﬂow rate through the process, and conce ptually is equal to

the average amount of time that a parcel of water spends in the process. This basic para-

meter relates the size of the process to the volume of material to be treated, and therefore

is a key parameter describing the economics of the process. The smaller the HRT, the

more economical the process is to construct.

Solids residence time (SRT), also known as the mean cell residence time (MCRT) or

sludge age, is the average amount of time that the biomass resides in the process from

when it is produced by microbial growth to when it is removed by deliberate wasting

or by loss with the efﬂuent. SRT is computed as the ratio of the mass of biomass within

the process divided by the mass wasted or lost from the process per unit time. The SRT is

basically the replacement growth rate of the biomass. For example, an SRT of 10 days

means that one-tenth of the biomass is replaced by growth each day. Therefore, a low

SRT implies a high growth rate, and vice versa. In terms of microbial kinetics, the SRT

for a steady-state process is the same as the net growth rate described in Chapter 11.

Because setting the SRT controls the net growth rate, it is the key parameter that controls

the biology of the process.

Under optimum growth conditions (in particular, high substra te concentrations) micro-

organisms can reproduce as fast as once every 20 minutes. A common misconception

among wastewater treatment plant operators is that high growth rate (being in the log

growth phase in terms of the batch microbial growth curve) is a desirable operating

goal. However, this is false for several reasons. One is that high growth rate implies

high substrate concentration, and therefore high efﬂuent BOD. On the contrary, it is essen-

tial to operate in the declining growth phase, which implies low substrate concentration.

Under this condition the microbes are ‘‘starved’’ for substrate. This causes low growth and

high SRT. The second reason for low growth rates is that the suspended or attached

growth biological wastewater treatme nt processes depend on the ability of the microbes

to produce exocellular polysaccharides which enable them to stick together (to form

‘‘ﬂocs’’) or to solid surfaces (to form ‘‘bioﬁlms’’), making it possible to separate the solids

from the wastewater and thus to decouple HRT from SRT.

The ﬂoc- or bioﬁlm-forming behavior is important because it makes it easy to retain

the biomass in the wastewater treatment process much longer than the wastewater itself.

For example, consider a process operated with an SRT of about 10 days, to achieve a low

enough efﬂuent BOD. If this process were operated in a completely mixed reactor, it

would have to also have an HRT of 10 days. That is, to treat 1 million gallons of waste-

water per day would require a tank with a volume of 10 million gallons. However, if it

were possible to keep the biomass in the reactor longer than the wastewater, it would be

possible to build a muc h smaller tank. The attached-growth processes accomplish this by

growing the biomass attached to a solid material as a bioﬁlm. Suspended growth processes

retain the biomass by using a sedimentation tank to trap the solids and then pump them

back to the reactor. The biomass in the reactor requires only a matter of hours to absorb or

WASTEWATER TREATMENT 585

otherwise remove the substrate from the wastewater. The puriﬁed wastewater can then

be discharged as efﬂuent. By separating the biomas s it is possibl e to have an HRT on

the order of several hours and an SRT of days. As a result, the treatment process can be

made to be a small fraction of the size it would otherwise have to be. In the example

just given, if the HRT were about 6 hours, the volume needed to treat 1 million gallons

per day would be just 250,000 gallons instead of 10 million gallons.

The microorganisms that make up the ﬂoc or bioﬁlm structure in biological wastewater

treatment produce the exocellular polysaccharide only under conditions of ‘‘starvation’’

and low net growth rate, corresponding to the low substrate concentrations that go with

high SRT. If the process is operated close to the minimum SRT, the substrate concentr a-

tion in the process will increase toward the inﬂuent concentration. At high substrate con-

centrations, the microbes will show less tendency to form ﬂocs or bioﬁlm. Without the

polysaccharide to help the bacteria to agglomerate into ﬂocs, they will grow dispers ed

in the wastewater, increasing efﬂuent turbidity, suspended solids, and BOD.

Flocculation behavior makes sense for bacterial survival. When an organism emits

some substance outside its boundaries, there is a cost that must be accompanied by a

return. Only under conditions of scarcity is this investment worthwhile for the microbe.

The beneﬁts are: (1) Entrapment of particulate substrate is enhanced; and (2) secretion of

exocellular digestive enzymes by a single cell could result in most of that enzyme diffus-

ing uselessly away from the cell, and a large fraction of any dissolved substrate formed by

digestion of the particle would also diffuse away. Within a ﬂoc or bioﬁlm, the bacteria are

cooperating by releasing enzymes that beneﬁt them collectively.

16.1.2 Attached-Growth Systems

The ﬁrst large-scale success with biological wastewater treatment was achieved midway

through the nineteenth century using an attached-growth process now referred to as trick-

ling ﬁlter technology (Figure 16.5). The operative biochemical agent within these

Figure 16.5 Attached-growth wastewater treatment system.

586

BIOLOGICAL APPLICATIONS FOR ENVIRONMENTAL CONTROL

systems develops as a thin microbial layer, commonly known as a bioﬁlm, which grows in

an attached fashion on the surface of stationary support media (see the media shown in

Figure 16.6) and over which the incoming wastewater is then continuously distributed and

streamed (see Figure 16.7). In turn, these attached-growth bioﬁlters will then sorb, ﬁlter,

and degrade waste contaminants as they trickle across their extensive attached-growth

surface.

Compared with mos t other waste-processing strategies, trickling ﬁlters are fairly sim-

ple in design and operation, and as a result they still ﬁnd considerable use (Water Envir-

onment Fe deration, 1991). While their overall effectiveness may be somewhat lower than

that of other processing strategies (e.g., suspended-growth systems), the attached nature of

these bioﬁlms does provide several complementary beneﬁts. Since the attached bioﬁlm

stays inside the reactor, there is less need to provide any sort of recycling process to return

solids from the clariﬁer (as must be done in suspended-growth systems). Trickling ﬁlter

systems also encounter fewer problems retaining their attached biomass during high-ﬂow

periods, whereas a suspended-growth reactor might overload the settler hydraulically,

resulting in solids loss in the efﬂuent. In many instances, and particularly in nitrifying

Figure 16.6 Attached growth bioﬁlm media options: (a) rock, (b) random packed plastic, and (c)

nested modular plastic bundle.

Figure 16.7 Attached growth wastewater treatment distributor.

WASTEWATER TREATMENT 587