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III. Agricultural Practices and Their Impact on Subsurface Habitats

III. Agricultural Practices and Their Impact on Subsurface Habitats

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E. L. MADSEN



36



lows describes agricultural practices that occur within the “physical system” of

Fig. 5. Emphasis is given to the influences and flows as they impinge on one

particular external system, groundwater.



TYPES

OF AGRICULTURAL

PRACTICES

This section discusses the mechanism(s) by which agricultural practices influence physical, chemical, and hydrologic conditions in the subsurface habitat

(Fig. I). Agricultural practices change in time and space, while the groundwater

habitat passively receives inputs from above (see Fig. 6). As was clear from

Section 1I.A and Figs. 2 and 4, the subsurface habitat represents an unusual union

between terrestrial and aquatic environments with often discontinuous and intermittent water flow from recharge areas. Entrainment of solutes (applied to or generated within surface soils) is virtually the only mechanism by which agricultural

practices impact the subsurface environment and its microbial inhabitants. Even

deep plowing activities such as moling and chiseling (see this section and

Section III.A.2; Briggs and Courtney, 1985; Loomis and Connor, 1992) fail to

penetrate through the soil habitat to directly transfer energy or materials to the

underlying subsurface. Thus, water management practices emerge as the principal

means by which agriculture influences the subsurface (Fig. 6). However, all of the

other management practices (i.e., those involving soils, crops, pests, and livestock) may have significant indirect effects both by altering rates of water infil-



Soil Habitat

Key agricultural practices:

I



I



Hydrologic

llnk between soil

and subsurface



I







1. Water management(espec~aiiy



Irrigation, drainage, and tillage)

may modifv the amount. extent.

depth, location, temperature,and

timing of Infiltrating water

2. Soil, crop, pest, and animal

management may modify the

compositonof intiitratingwaters,

especially, salts, nutrients,

organlc carbon, metals,

pesticides, and other chemlcal

components



SubsurfaceHabitat



Figure 6. The hydrologic link between the soil habitat, where agricultural practices occur, and

the subsurface habitat which supports a responsive biotic community that is almost exclusively

microbial.



SUBSURFACE MICROBIAL ECOLOGY



37



trating through soil and by altering the chemical composition of waterborne materials reaching the subsurface habitat.



1. Water Management

Water availability represents one of the main controls on crop growth. Plants

require water for two main reasons: to maintain cell turgor pressure and to supply

nutrients (Briggs and Courtney, 1985). Water deficiencies lead, under extreme

conditions, to loss of turgidity and wilting of the plant. Under less extreme water

deficiency conditions, growth may be inhibited by lack of nutrients and by diminished photosynthetic efficiency. Excesses of water may also occur, however. Crop

plants obtain most of their water from the soil, a complex, porous matrix in which

both air and water reside in the same pores. When water is present in abundance,

air may be excluded from the pores and plants may suffer from lack of oxygen.

With the exception of wetland rice plants (Tivy, 1990), physiological problems

induced by anaerobic conditions may ensue for the crop (Briggs and Courtney,

1985).

In many parts of the world a soil water surplus, for part or all of the year, limits

the amount of time available for crop growth. Some form of drainage is, therefore,

necessary for successful crop growth. The basic aim of all drainage systems is

to remove soil water so that soil aeration can be achieved. This, in turn, alleviates toxic anaerobic conditions and promotes deeper, more extensive root development (Tivy, 1990). Essentially three strategies exist for draining soil: (1) improve the vertical movement of water; (2) improve the lateral water movement;

and (3) lower the regional water table (Briggs and Courtney, 1985). These drainage strategies are pursued by carrying out one or several of the following procedures: “moling” (formation of an unlined subsurface cylindrical channel, approximately 0.5 m deep that is created by drawing a bullet-shaped implement

through the soil); “subsoiling” (which uses techniques much like moling to shatter impermeable pan layers beneath the normal plowing depth); pipe drains (which

convey excess water away from subsoils; pipe drains are installed by digging

trenches and lining them with tiles or top-perforated plastic pipes prior to being

covered over); and open ditches (Briggs and Courtney, 1985; Tivy, 1990).

In other parts of the world there is a deficiency of soil water for crop production

for part or all of the year. Agriculture in these arid and semiarid regions relies on

irrigation, the transport of water from a supply source to land whose atmospheric

input of water fails to keep pace with evapotransporational losses. Three general

methods of irrigation may be identified: surface methods, overhead methods, and

subsurface methods (Briggs and Courtney, 1985). By far, the most widely used

are surface methods of application for, in general, these involve relatively lowcost technology (i.e., gravity flow of water) and are easy to apply over a wide area.



38



E. L. MADSEN



Surface flooding may be achieved by damming and diverting main streams (uncommon in North America) and also by distributing water over the surface via

furrows. The water seepage occurs through the base and sides of furrows and, via

capillary action, reaches ridges within which the crops are planted (Briggs and

Courtney, 1985).

Overhead methods of irrigation are varied. Water is normally sprinkled onto the

soil surface from nozzles. The nozzles may be mounted on sprinkler units that are

static, rotating, or traveling. Overhead irrigation often has the advantage of being

independent of surface topography (Briggs and Courtney, 1985). Trickle (or drip)

irrigation involves the discharge of small amounts of water from small orifices

located on or immediately below the soil surface near the crop roots. Trickle irrigation strives for highly effective use of water while minimizing water loss and

soil disturbance. Finally, subirrigation is an expensive, specialized irrigation practice that uses damming procedures and drains to manage the water table level so

as to bring the capillary fringe (see Sections I and 11) within the root zone of the

crop (Tivy, 1990; Briggs and Courtney, 1985).

There are four key concerns in managing water for agricultural purposes: the

mechanics and hydraulics of distributing water; the timing of these water fluxes;

the volume of these water fluxes; and the quality of the water (Briggs and Courtney, 1985). These four concerns apply to both drainage and irrigation practices

and they raise several fundamental issues about the environmental impact of water

management on the subsurface habitat.

1. Water (like all matter) is neither created nor destroyed-its mass is conserved. Whenever water is moved, the source necessarily becomes initially drier

and the receiving area becomes wetter. This simple truism means that assessments

of the environmental or ecological impacts of irrigation practices necessarily must

consider both the habitat that provides the water and the one that receives it.

2. No water used for irrigation is free of dissolved or suspended materials.

Thus, whenever water is conveyed, so also are conveyed its accompanying chemical constituents. Of particular concern is the salinization of soils that are under

irrigation in arid areas. As irrigation waters evaporate, salts (commonly of sodium, calcium, magnesium, chloride, sulfate, bicarbonate, as well as a variety of

trace elements) may accumulate over time. High salt concentrations in soil may

contribute to the development of impermeable soil layers (pans) and may be deleterious to both soil structure and crop growth.

As just discussed and shown in Fig. 6, water management practices are the

single most influential means by which agriculture affects subsurface microorganisms. Rows 2-5 of Table I11 (summarized from Loomis and Connor, 1992; Tivy,

1990; Briggs and Courtney, 1985; Soule ef al., 1990) provide an overview of

water management practices and their impact on the subsurface habitat.



SUBSURFACEMICROBIAL ECOLOGY



39



2. Soil Management

Physical modification of the soil resource, via tillage practices, is designed to

create favorable conditions for crop growth and development. Tillage is carried

out for three main reasons: (1) physical preparation of the seedbed (i.e., by plowing or harrowing) to break up soil aggregates; ( 2 ) removal of crop residue and

weeds by reducing their size and burying them to promote decay and nutrient

cycling; and (3) improvement of rooting and drainage conditions (i.e., by deep

plowing) (Briggs and Courtney, 1985). A variety of tillage systems have been

developed, each of which may be implemented according to the prevailing agricultural conditions (geographic location, crop planted, climate, soil type, and a

variety of socioeconomic factors).

According to Loomis and Connor ( I 992), “primary (or conventional) tillage”

utilizes a mold board plow, often in combination with a disk plow to dig into and

invert top soil. “Secondary tillage” is the preparation of seed beds with field cultivators, light disks, and spring- or spike-toothed harrows. These implements reduce the size of soil peds and leave the soil smoother and firmer for improved

contact among seed, soil, and its moisture. Conventional tillage approaches contrast with “reduced till” and “no till” systems in which the degree of plowing is

diminished and reliance on herbicides for weed control is increased.

Rows 6-9 of Table 111 provide an overview of soil management practices and

their impact on the subsurface habitat. The principal means by which soil management methods impact ground water is by influencing the chemical composition

and flow rates of infiltrating water.



3. Crop Management

Crop management begins with the sowing of seeds, continues with crop maintenance during growth and development, and ends with crop harvest, storage, and

distribution (Tivy, 1990). During seed sowing, a mechanized planter often opens

a furrow in the prepared soil seed bed, places the seed in the exposed moist soil,

covers the planted seed, and then often packs the soil down to assure firm

seed-soil contact. In no-till systems, the crop is planted (“drilled”) directly into

the soil through residue from the previous crop.

Soil fertilization is an essential component of crop management to assure nutritional sufficiency for plant growth. The selection of type, amount, timing, and

method of fertilizer application is determined by a variety of considerations including the crop type, the nature of the fertilizer, soil conditions, and weather. A

generalized listing of common fertilizer applications follows (after Briggs and

Courtney, 1985): ( I ) broadcast [application of fertilizer (often pelletized) to the

soil surface before the crop emerges]; ( 2 ) plowing in (application of fertilizer to



P

0



Table I11

Agricultural Practices“and Their Impact on Conditionsin the Subsurface Habitat



Type of

agricultural practice

Water management

(exerts a direct” influence on the hydrologic link between soil and the

subsurface)



Key references

documenting impact

of agricultural practices

on soil or groundwater



Practice



Impact on groundwater flux and types of solutes entrained



None (only climate and unmodified soil and vegetation

govern water flux)



No change in ambient fluxes of water from surface to subsurface; naturally occurring inorganic and organic solutes are transported in recharge water



Land drainage



Decrease in flux of water and accompanying inorganic and organic solutes from soil to the subsurface



Danielpool et al. ( 1 99 I );

Schot and Molenaar

( 1992); Utermann et al.



Surface flood irrigation



May increase flux of water to the subsurface; intermittent flood irrigation may cause salinization of soil; high-volume flooding may transport salts to the subsurface

Salinization of soils may occur; subsequent flooding may transport salts

to subsurface

May physically influence the subsurface by lowering the water table, increasing the extent of vadose zone, and (in some situations) causing

land subsidence



Frenkel and Meiri (1985);

Magaritz and Nadler



( 1990)



Soil management (exerts an indirecth influence on the hydrologic link

between soil and the

subsurface)



Overhead, drip, and subsurface

imgation

Withdrawal of water from subsurface and surface

reservoirs

None



No change in ambient fluxes of water and naturally occurring inorganic

and organic solutes



(1993);

McTerman and Mize

(1992); Umali (1993)

Bouwer (1981); Carbognin

( 1985)



Plowing:

Chisel

Moldboard

Disk



Field cultivation

Cultivator

Harrows

Tillers

Hoes

Reduced till and no till

systems



Crop management (exerts and indirecth

influence on the hydrologic link between soil and the

subsurface)



Sowing, cultivation, mulching,

manure application, fertilizer application, green manuring, harvesting



Soil compaction and reduction of soil porosity caused by tractor tires

may decrease water infiltration and flux to subsurface.

Enhanced infiltration may increase water flux to subsurface.

Mixing of soils and crop residues may enhance their decay, hence accelerated nutrient release to soil solution and perhaps to groundwater.

Increased soil porosity may reduce soil thermal conductivity hence

raise soil temperatures and the temperature of water infiltrating to the

subsurface.

Under certain circumstances, repeated plowing may cause impermeable

layers (pans) beneath the soil surface to form, hence decrease flux of

water to subsurface.

Soil compaction and reduction of soil porosity caused by tractor tires

may decrease water infiltration and flux to subsurface.

Altered seedbed aspect may increase radiation received and decrease radiation losses; resultant increased soil temperatures may warm the

waters infiltrating to the subsurface.

Decrease in water and wind erosion of soil may enhance or diminish

water flux to the subsurface.

Soil temperatures may increase because thermal turbulent transfer may

decrease, this may warm the water infiltrating to the subsurface.

However, reflection of sunlight may reduce soil temperatures, thus cooling water infiltrating to the subsurface.

See the soil management portion of this table.

The major additional element of crop management is the presence of

roots and shoots of growing crops. These may alter the physical and

hydrologic properties of soil. In addition, the primary production,

exudation, decay, and imperfect uptake of fertilizer amendments

which are characteristic of crop management practices may release

additional organic and inorganic compounds to soil solution which,

in turn, may leach into the subsurface habitat



Vanderzee and Boesten

(1991)



Parkin and Meisinger

( 1989)



Isensee et nl. ( 1990)



Alfoldi (1983); Goodrich

et al. (1991); Spalding

and Exner ( I993 )



( continues)



Table Ill-Continued

Key references

documenting impact

of agricultural practices

on soil or groundwater



Type of

agricultural practice



Practice



Impact on groundwater flux and types of solutes entrained



Pest management (exerts an indirect” influence on the hydrologic link

between soil and the

subsurface)



Physical weed control (tillage,

burning, etc.), crop rotation,

trap crops, other IPM procedures, insecticides, fungicides, acaricides and other

pesticides, fumigation



See the water, soil, and crop management portions of this table.

The major additional characteristics of pest management are the addition of pesticides and related carriers and residues to soil, soil solution, plants, and plant tissues. These may, under some circumstances,

leach into subsurface environments.



Domagalski and Dubrovsky ( 1992): Jury and

Gruber ( 1989, 1990);

Lawrence et a/. (1993);

Loague et crl. ( 1990);

Ritter (1990); Shoemaker et d.( 1990); Varshney et crl. (1993): Villeneuve et ul. ( 1990)



Livestock management

(exerts an indirect”

influence on the hydrologic link between soil and the

subsurface)



Water management, soil management (none, plowing,

tilling, see above), crop

management (none, forage,

feed, see above), grazing,

manure management, feeds,

feed supplements (hormones, antibiotics, etc.),

primary harvest ( i t . , biomitss of livestock animals),

secondary harvest ( i t . , livestock products such as milk,

fiber, eggs), pest management. livestock medicine



See comments for water, soil, crop, and pest management.

Livestock management practices have additional effects such as soil

compaction and erosion (imposed by various traffic and grazing regimes); nutrients released as manures and urine; and other logistical aspects of rearing, maintaining, transporting, and harvesting livestock

populations



Headworth ( 1989); Sangodoyin and Ogedengbe

(1991)



“References for agricultural practices include Loomis and Connor (1992); Tivy (1990); and Briggs and Courtney ( 1985)

’See Fig. 6 and text in Section 111.



SUBSURFACEMICROBIAL ECOLOGY



43



the surface followed by mixing into the topsoil by plowing); (3) sideband (fertilizer application in bands adjacent to the seed); (4) contact placement (fertilizer

application in direct contact with the seed); (5) side-dressing (fertilizer placement

in narrow rows at the surface after crop emergence); and (6) top-dressing (general

application of fertilizer to the crop after emergence).

During crop growth, a variety of crop and soil maintenance as well as weed

removal practices may be undertaken. Again, the specific type of farm machinery

actually used and overall management practices are site, farmer, and climate specific. But overall, weed control can be accomplished through several types of soil

cultivation practices (see earlier). These include dense arrays of small spring tines,

rotary hoes, and tractor-mounted arrays of spear- or sweep-pointed shanks designed to till in between crop rows (Loomis and Connor, 1992). Herbicides are

also used widely for weed control (see the following discussion).

Row 10 of Table 111 provides an overview of the input of crop management and

the subsurface habitat. In essence, crop management practices influence the subsurface habitat by two independent mechanisms. First, the physical structure of

soil (hence the infiltration rates of water) is altered by farm machinery traffic passing over the soil, by cultivation implements, and by the penetration of soil by roots

and shoots of the growing crop plants. Second, the solutes in soil that may be

conveyed to the subsurface by infiltrating water are determined by the organic and

inorganic compounds present in the soil as a result of fertilizer amendments and

crop growth and decay.



4. Pest Management

The steps that are taken in agriculture to foster the growth of desirable organisms (crops) also foster the growth of undesirable organisms (pests). From an

ecological viewpoint, the presence of pests in agriculture is unavoidable because

the physical, chemical, nutritional, and hydrologic resources made available to

crops represent a bounty of resources for opportunistic noncrop biota. These include weeds, animals (especially insects; but also slugs, nematodes, rodents, birds,

and others), and microorganisms (especially plant pathogens that include fungi,

bacteria, and viruses) (Briggs and Courtney, 1985; Tivy, 1990). According to

Briggs and Courtney (1985), it has been estimated that weeds, animals, and pathogens may account for a reduction of global preharvest crop yields that approach

50%. The major mechanism of yield reduction is reducing leaf areas, hence photosynthesis. Weeds also compete with crop plants for sunlight, water, and nutrients.

Clearly, pest management is an essential component of agriculture. Ecological

methods of pest control are implicit in all agricultural practices and are explicit in

integrated pest management (IPM) strategies. All pests are susceptible to their

own arrays of environmental stresses, diseases, and predators. All pests generally

do less damage to well-managed, rapidly growing crops than, for example, to



44



E. L. MADSEN



those deficient in nutrients (Loomis and Connor, 1992). The wide variety of

weeds, animals, and microorganisms which threaten agricultural crops demand a

correspondingly wide range of crop protection methods. These include five main

techniques, each of which may be used to suppress, deter, eradicate, or prevent

infestation: ( I ) direct control (i.e., weeding); (2) crop cultivation methods;

(3) chemical control; (4) biological control; and (5) habitat removal (Briggs and

Courtney, 1985).

Weed management strategies center on limiting the size of the seed bank

through control of weed reproduction (Loomis and Connor, 1992). Sanitation is

important because small untended weed populations in I year can cause crop

losses over a number of subsequent years. Tillage is a major means for reducing

weed plant populations that have germinated and grown within stands of agricultural crops (Loomis and Connor, 1992; tillage practices have been described earlier). Herbicides have reduced or replaced tillage weed control practices in many

cropping systems. Herbicides enable weed control to be accomplished more

quickly, more timely, less expensively, and with significantly less energy use than

with tillage (Briggs and Courtney, 1985). Herbicides include synthetic organic

chemicals that are highly selective to particular groups of plants (i.e., monocotyledonous vs dicotyledonous). Other herbicides are formulated to act as general

toxins-by inhibiting physiological processes common to all green plants (i.e.,

photosynthesis and cell elongation and division). Depending on mode of action,

target weeds, and cropping systems, herbicides may be applied with a variety of

spraying implements (mounted on knapsacks, booms, tractors, and airplanes). The

application may occur prior to weed growth (pre-emergence herbicides) or postemergence to weed leaves where they may act on contact or be translocated

through the plant to roots and shoots.

Animal and microbial pest management practices, like those of weed management, rely to a large degree on crop cultivation methods. Tillage, irrigation, crop

rotation, burial of crop residues, and related practices alter the crop environment

such that conditions are adverse to the growth and reproduction of insect and

microbial pests. By understanding specific details of a pest’s life cycle (such as

alternate hosts, overwintering stages, or susceptibility to desiccation), management practices can be directed to reduce the pest population, hence its detrimental

effect on crops. Using much the same approach, biocides (directed toward insects,

mites, nematodes, fungi, and bacteria, among others) have been developed which

target essential physiological and biochemical functions specific to the pest of

interest. For instance, organophosphorus and carbamate insecticides act on the

nervous system of insect pests by inhibiting a key enzyme, acetylcholinesterase,

at the nerve synapse. Both contact and systemic biocides are applied at relatively

low concentrations (part per million, i.e., kilogram per hectare of land) by aerial

application to plants or as solutions or granules applied to soil. To act, some pesticides must be ingested by the pest (i.e., by an insect consuming insecticide-



SUBSURFACE MICROBIAL ECOLOGY



45



coated plant leaves) while others must come into direct physical contact with the

surface of the pest.

Row 1 1 of Table I11 summarizes pest management practices and their impact

on the subsurface habitat. Pest management practices influence the subsurface indirectly by affecting the chemical composition of waters that may percolate

through soil to reach ground water.



5. Livestock Management

By definition, the variety of agricultural animals (i.e., cattle, sheep, pigs, goats,

buffalo, horses, donkeys, mules, and poultry) graze on products of agricultural

crops. Livestock reside one trophic level above the crops, which carry out primary

production. Thus, implicit in livestock management is a degree of complexity that

surpasses that of the four types of management described earlier (Briggs and

Courtney, 1985; Tivy, 1990). In order to support livestock, water, soil, crops, and

pests need to be managed. This is true even if the livestock are supported by lowinput range land. Furthermore, animal-specific requirements must also be met.

These pertain to animal growth, reproduction, physiology, behavior, maturation,

and both primary (i.e., animal biomass) and secondary (i.e., milk and eggs)

harvest.

Livestock management techniques vary considerably with the type of animal,

climate, soil type, moisture regime, and infrastructures for use, distribution, and

marketing the animal products. As in crop management, the overall goal in livestock management is to maximize the yield of desired product and minimize input

of time, energy, and materials, while maintaining the management system (i.e.,

soil, water, crops, and other related resources) in a sustainable state. Major considerations in livestock include growth of, harvest, storage, curing, and distribution

of fodder (crops harvested then fed to livestock); growth of forage (crops grazed

in situ by livestock); dietary considerations (especially to ensure mineral and lysine sufficiency for both ruminants and nonruminants); herd maintenance; disease

development and transmission; animal reproductive cycles; growth and harvest of

the animal and/or animal products; hygiene for the animals and animal products;

hygiene for animal wastes (especially urine and manures); handling, distribution,

and disposal of animal manures (especially for feedlot rearing of beef cattle); grazing regime for forage animals (this includes free range, set-stocking, rotational,

strip grazing, and zero grazing); and minimizing damage to soil structure and

vegetation caused by the trampling of soil by animals (Briggs and Courtney, 1985;

Tivy, 1990).

A full and detailed treatment of livestock management strategies and procedures is beyond the scope of this chapter. For additional information, readers are

referred to Ensminger (1991) and Curtis (1983). The overview presented here and

Row 12 of Table 3 succinctly indicate the complexity of livestock management



46



E. L. MADSEN



practices and their primary mechanisms of altering surface environments; hence

their potential impacts on groundwater and the subsurface habitat.



IV. IMPACT OF AGRICULTURAL PRACTICES

ON SUBSURFACEMICROBIAL ECOLOGY

Thus far, the fundamental and independent characteristics of subsurface microbial ecology (Section 11) and agricultural practices (Section 111) have been outlined. In discussing how these two entities overlap and interact, it is appropriate

to remind the reader of information and concepts in Figs. 1 through 6 and the

chapter overview presented in Section I.



A. A HISTORICAL

PERSPECTIVE

FOR INQUIRY

INTO

SUBSURFACE

VERSUS SURFACE

HABITATS

Human curiosity, ingenuity, and material gain are among the primary motivations for scientific investigation of the variety of habitats in the biosphere. Clearly,

grasslands, forests, mountains, oceans, lakes, ponds, rivers, and streams, their

physical resources, and their flora and fauna have been critical for the development of civilizations (Ehrlich er al., 1977; Odum, 1971; Wetzel, 1983; Nybakken,

1988). Since early visualization of microorganisms by Robert Hooke in 1664, the

ecological role of microorganisms in these key surface habitats has become evident (Atlas and Bartha, 1993; Brock er al., 1994; Odum, 1971). But why were

both the subsurface ecosystem and its inhabitants left undiscovered (Ghiorse and

Wilson, 1988) until the latter part of the 20th century? One answer to this question

may be that, unlike much of the rest of the biosphere, subsurface ecology had little

to do with human activities. After all, there is really nowhere for humans to go

underground without miners’ tools. Furthermore, other than microorganisms,

there is no wildlife to speak of in the subsurface. Also, unlike the rest of the

biosphere the subsurface has until recently been considered to be an inert, lifeless

zone (Ghiorse and Wilson, 1988; Madsen and Ghiorse, 1993; Chapelle, 1993).

Aside from supplying bountiful, reliably pure sources of drinking water, the subsurface habitat has not traditionally been known to provide vital functions characteristic of other portions of the biosphere (e.g., photosynthesis, decomposition,

and cycling of nutrients; see Section II.B.3 and Fig. 4).

In the soil habitat, [it has virtually been impossible to overlook the microbially

mediated annual dynamics of plant growth, biomass decay, cycling of carbon,

nitrogen and phosphorous; uptake and release of other nutrients; humification;

etc.]. In contrast, there has traditionally been no need to even suspect that subsur-



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