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Soil Biology The Soil Biology Primer

Chapter 1: THE SOIL FOOD WEB
SOIL BIOLOGY AND THE
LANDSCAPE THE FOOD WEB: O...
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Soil Biology

Th e Soil Biology Pr im e r

Ch a pt e r 1 : TH E SOI L FOOD W EB

By Elaine R. I ngham

SOI L BI OLOGY AN D TH E LAN D SCAPE

An incredible diversit y of organism s m ake up t he soil food web. They range in size from t he t iniest one-

celled bact eria, algae, fungi, and prot ozoa, t o t he m ore com plex nem at odes and m icro- art hropods, t o t he

visible eart hworm s, insect s, sm all vert ebrat es, and plant s.As t hese organism s eat , grow, and m ove t hrough

t he soil, t hey m ake it possible t o have clean wat er, clean air, healt hy plant s, and m oderat ed wat er flow.

There are m any ways t hat t he soil food web is an int egral part of landscape processes. Soil organism s

decom pose organic com pounds, including m anure, plant residue, and pest icides, prevent ing t hem from

ent ering wat er and becom ing pollut ant s. They sequest er nit rogen and ot her nut rient s t hat m ight ot herwise

ent er groundwat er, and t hey fix nit rogen from t he at m osphere, m aking it available t o plant s. Many

organism s enhance soil aggregat ion and porosit y, t hus increasing infilt rat ion and reducing runoff. Soil

organism s prey on crop pest s and are food for above- ground anim als.

The soil e nvir onm e nt . Organism s live in t he m icroscale environm ent s wit hin

and bet ween soil part icles. Differences over short dist ances in pH, m oist ure, pore

size, and t he t ypes of food available creat e a broad range of habit at s.

Cr e dit : S. Rose and E.T. Elliot t

TH E FOOD W EB: ORGAN I SM S AN D TH EI R I N TERACTI ON

The soil food web is t he com m unit y of organism s living all or part of t heir lives in

t he soil. A food web diagram shows a series of conversions ( represent ed by

arrows) of energy and nut rient s as one organism eat s anot her ( see food web

diagram ) .

All food webs are fueled by t he prim ary producers: t he plant s, lichens, m oss,

phot osynt het ic bact eria, and algae t hat use t he sun’s energy t o fix carbon dioxide from t he at m osphere.
Most ot her soil organism s get energy and carbon by consum ing t he organic com pounds found in plant s,

ot her organism s, and wast e by- product s. A few bact eria, called chem oaut ot rophs, get energy from nit rogen,

sulfur, or iron com pounds rat her t han carbon com pounds or t he sun.

As organism s decom pose com plex m at erials, or consum e ot her organism s, nut rient s are

convert ed from one form t o anot her, and are m ade available t o plant s and t o ot her soil

organism s. All plant s – grass, t rees, shrubs, agricult ural crops – depend on t he food

web for t heir nut rit ion.

W H AT D O SOI L ORGAN I SM S D O?

Growing and reproducing are t he prim ary act ivit ies of all living

organism s. As individual plant s and soil organism s work t o survive, t hey depend on

int eract ions wit h each ot her. By- product s from growing root s and plant residue feed soil

organism s. I n t urn, soil organism s support plant healt h as t hey decom pose organic m at t er,

cycle nut rient s, enhance soil st ruct ure, and cont rol t he populat ions of soil organism s including crop pest s.

( See t able of funct ions of soil organism s.)

ORGAN I C M ATTER FUELS TH E FOOD W EB

Soil organic m at t er is t he st orehouse for t he energy and nut rient s used by plant s and ot her organism s.

Bact eria, fungi, and ot her soil dwellers t ransform and release nut rient s from organic m at t er ( see phot o) .

Organic m at t er is m any different kinds of com pounds – som e m ore useful t o organism s t han ot hers. I n

general, soil organic m at t er is m ade of roughly equal part s hum us and act ive organic m at t er. Act ive organic

m at t er is t he port ion available t o soil organism s. Bacteria t end t o use sim pler organic com pounds, such as

root exudat es or fresh plant residue. Fungi t end t o use m ore com plex com pounds, such as fibrous plant

residues, wood and soil hum us.

I nt ensive t illage t riggers spurt s of act ivit y am ong bact eria and ot her organism s t hat consum e organic m at t er

( convert it t o CO2) , deplet ing t he act ive fract ion first . Pract ices t hat build soil organic m at t er ( reduced t illage

and regular addit ions of organic m at erial) will raise t he proport ion of act ive organic m at t er long before

increases in t ot al organic m at t er can be m easured. As soil organic m at t er levels rise, soil organism s play a

role in it s conversion t o hum us—a relat ively st able form of carbon sequest ered in soils for decades or even

cent uries.
FOOD SOURCES FOR SOI L ORGAN I SM S

“ Soil organic m at t er” includes all t he organic subst ances in or on t he soil. Here are t erm s used t o describe

different t ypes of organic m at t er.

Living or ga nism s: Bact eria, fungi, nem at odes, prot ozoa, eart hworm s, art hropods, and living root s.

D e a d pla nt m a t e r ia l; or ga n ic m a t er ia l; de t r it u s; su r fa ce r e sidu e : All t hese t erm s refer t o plant ,

anim al, or ot her organic subst ances t hat have recent ly been added t o t he soil and have only begun t o show

signs of decay. Det rit ivores are organism s t hat feed on such m at erial.

Act ive fr a ct ion or ga nic m a t t er : Organic com pounds t hat can be used as food by m icroorganism s. The

act ive fract ion changes m ore quickly t han t ot al organic m at t er in response t o m anagem ent changes.

La bile or ga nic m a t t er : Organic m at t er t hat is easily decom posed.

Root e x uda t e s: Soluble sugars, am ino acids and ot her com pounds secret ed by root s.

Pa r t icu la t e or ga nic m a t t er ( POM ) or Light fr a ct ion ( LF) or ga nic m a t t e r : POM and LF have precise

size and weight definit ions. They are t hought t o represent t he act ive fract ion of organic m at t er which is

m ore difficult t o define. Because POM or LF is larger and light er t han ot her t ypes of soil organic m at t er, t hey

can be separat ed from soil by size ( using a sieve) or by weight ( using a cent rifuge) .

Lignin: A hard- t o- degrade com pound t hat is part of t he fibers of older plant s. Fungi can use t he carbon

ring st ruct ures in lignin as food.

Re ca lcit r a nt or ga n ic m a t t e r : Organic m at t er such as hum us or lignin- cont aining m at erial t hat few soil

organism s can decom pose.

H u m u s or h um ifie d or ga nic m a t t er : Com plex organic com pounds t hat rem ain aft er m any organism s

have used and t ransform ed t he original m at erial. Hum us is not readily decom posed because it is eit her

physically prot ect ed inside of aggregat es or chem ically t oo com plex t o be used by m ost organism s. Hum us is

im port ant in binding t iny soil aggregat es, and im proves wat er and nut rient holding capacit y.
 Com pone nt s of Soil Or ga n ic M a t t e r

W H ERE D O SOI L ORGAN I SM S LI VE?

The organism s of t he food web are not uniform ly dist ribut ed t hrough t he soil.

Each species and group exist s where t hey can find appropriat e space, nut rient s,

and m oist ure. They occur wherever organic m at t er occurs – m ost ly in t he t op few

inches of soil ( see figure) , alt hough m icrobes have been found as deep as 10

m iles ( 16 km ) in oil wells.

Soil organism s are concent rat ed:

Ar ound r oot s. The rhizosphere is t he narrow region of soil direct ly around root s ( see phot o) . I t is t eem ing

wit h bact eria t hat feed on sloughed- off plant cells and t he prot eins and sugars released by root s. The

prot ozoa and nem at odes t hat graze on bact eria are also concent rat ed near root s. Thus, m uch of t he nut rient

cycling and disease suppression needed by plant s occurs im m ediat ely adj acent t o root s.

Bact eria are abundant around t his root t ip ( t he rhizosphere) where t hey

decom pose t he plent iful sim ple organic subst ances. Cr edit : No. 53 from Soil

Microbiology and Biochem ist ry Slide Set . 1976 J.P. Mart in, et al., eds. SSSA,

Madison WI .
I n lit t er . Fungi are com m on decom posers of plant lit t er because lit t er has large am ount s of com plex, hard-

t o- decom pose carbon. Fungal hyphae ( fine filam ent s) can “ pipe” nit rogen from t he underlying soil t o t he

lit t er layer. Bact eria cannot t ransport nit rogen over dist ances, giving fungi an advant age in lit t er

decom posit ion, part icularly when lit t er is not m ixed int o t he soil profile. However, bact eria are abundant in

t he green lit t er of younger plant s which is higher in nit rogen and sim pler carbon com pounds t han t he lit t er

of older plant s. Bact eria and fungi are able t o access a larger surface area of plant residue aft er shredder

organism s such as eart hworm s, leaf- eat ing insect s, m illipedes, and ot her art hropods break up t he lit t er int o

sm aller chunks.

On h um u s. Fungi are com m on here. Much organic m at t er in t he soil has already been decom posed m any

t im es by bact eria and fungi, and/ or passed t hrough t he gut s of eart hworm s or art hropods. The result ing

hum ic com pounds are com plex and have lit t le available nit rogen. Only fungi m ake som e of t he enzym es

needed t o degrade t he com plex com pounds in hum us.

On t he sur fa ce of soil a ggr e ga t e s. Biological act ivit y, in part icular t hat of aerobic bact eria and fungi, is

great er near t he surfaces of soil aggregat es t han wit hin aggregat es. Wit hin large aggregat es, processes t hat

do not require oxygen, such as denit rificat ion, can occur. Many aggregat es are act ually t he fecal pellet s of

eart hworm s and ot her invert ebrat es.

I n spa ce s bet w e e n soil a ggr e ga t e s. Those art hropods and nem at odes t hat cannot burrow t hrough soil

m ove in t he pores bet ween soil aggregat es. Organism s t hat are sensit ive t o desiccat ion, such as prot ozoa

and m any nem at odes, live in wat er- filled pores. ( See Figure page 1.)

W H EN ARE TH EY ACTI VE?

The act ivit y of soil organism s follows seasonal pat t erns, as well as daily pat t erns. I n

t em perat e syst em s, t he great est act ivit y occurs in lat e spring when t em perat ure and

m oist ure condit ions are opt im al for growt h ( see graph) . However, cert ain species are

m ost act ive in t he wint er, ot hers during dry periods, and st ill ot hers in flooded

condit ions.

Not all organism s are act ive at a part icular t im e. Even during periods of high act ivit y, only a fract ion of t he

organism s are busily eat ing, respiring, and alt ering t heir environm ent . The rem aining port ion are barely

act ive or even dorm ant .

Many different organism s are act ive at different t im es, and int eract wit h one anot her, wit h plant s, and wit h

t he soil. The com bined result is a num ber of beneficial funct ions including nut rient cycling, m oderat ed wat er

flow, and pest cont rol.

TH E I M PORTAN CE OF TH E SOI L FOOD W EB

The living com ponent of soil, t he food web, is com plex and has different com posit ions in different

ecosyst em s. Managem ent of croplands, rangelands, forest lands, and gardens benefit s from and affect s t he

food web. The next unit of t he Soil Biology Prim er, “ The Food Web & Soil Healt h,” int roduces t he relat ionship

of soil biology t o agricult ural product ivit y, biodiversit y, carbon sequest rat ion and t o air and wat er qualit y.

The rem aining six unit s of t he Soil Biology Prim er describe t he m aj or groups of soil organism s: bact eria,

fungi, prot ozoa, nem at odes, art hropods, and eart hworm s. For m ore inform at ion about t he diversit y wit hin

each organism group, see t he list of readings at t he end of “ The Food Web & Soil Healt h” unit .

Ch a pt e r 2 : TH E FOOD W EB & SOI L H EALTH

By Elaine R. I ngham

H OW D O FOOD W EBS D I FFER?

Each field, forest , or past ure has a unique soil food web wit h a part icular proport ion of

bact eria, fungi, and ot her groups, and a part icular level of com plexit y wit hin each group of

organism s. These differences are t he result of soil, veget at ion, and clim at e fact ors, as well

as land m anagem ent pract ices. ( See figure of food webs in different ecosyst em s.)

TYPI CAL FOOD W EB STRUCTURES

The “ st ruct ure” of a food web is t he com posit ion and relat ive num bers of organism s in

each group wit hin t he soil syst em . Each t ype of ecosyst em has a charact erist ic food web

st ruct ure ( see t able of t ypical num bers of organism s in soil) . Som e feat ures of food web

st ruct ures include:

Th e r a t io of fu n gi t o ba ct e r ia is ch a r a ct er ist ic t o t he t ype of syst e m . Grasslands and agricult ural soils

usually have bact erial- dom inat ed food webs – t hat is, m ost biom ass is in t he form of bact eria. Highly

product ive agricult ural soils t end t o have rat ios of fungal t o bact erial biom ass near 1: 1 or som ewhat less.
Forest s t end t o have fungal- dom inat ed food webs. The rat io of fungal t o bact erial biom ass m ay be 5: 1 t o

10: 1 in a deciduous forest and 100: 1 t o 1000: 1 in a coniferous forest .

Or ga n ism s r e fle ct t h e ir food sou r ce . For exam ple, prot ozoa are abundant where bact eria are plent iful.

Where bact eria dom inat e over fungi, nem at odes t hat eat bact eria are m ore num erous t han nem at odes t hat

eat fungi.

M a na ge m e nt pr a ct ice s cha nge food w e bs. For exam ple, in reduced t illage agricult ural syst em s, t he rat io

of fungi t o bact eria increases over t im e, and eart hworm s and art hropods becom e m ore plent iful.

H OW I S TH E FOOD W EB M EASURED ?

The m easurem ent t echniques used t o charact erize a food web include:

Cou n t in g. Organism groups, such as bact eria, prot ozoa, art hropods, et c.; or subgroups, such as bact erial-

feeding, fungal- feeding, and predat ory nem at odes, are count ed and t hrough calculat ions, can be convert ed

t o biom ass.

Direct count s – count ing individual organism s wit h t he naked eye or wit h a m icroscope. All organism s

can be count ed, or only t he act ive ones t hat t ake up a fluorescent st ain ( Figure 3) .

Plat e count s – count ing t he num ber of bact erial or fungal colonies t hat grow from a soil sam ple.

M e a sur in g a ct ivit y le ve ls. Act ivit y is det erm ined by m easuring t he am ount of by- product s, such as CO2 ,

generat ed in t he soil, or t he disappearance of subst ances, such as plant residue or m et hane used by a large

port ion of t he com m unit y or by specific groups of organism s.

These m easurem ent s reflect t he t ot al “ work” t he com m unit y can do. Tot al biological act ivit y is t he sum of

act ivit ies of all organism s, t hough only a port ion are act ive at a part icular t im e.

Respirat ion – m easuring CO2 product ion. This m et hod does not dist inguish which organism s ( plant s,

pat hogens, or ot her soil organism s) are generat ing t he CO2 .

Nit rificat ion rat es – m easuring t he act ivit y of t hose species involved in t he conversion of am m onium t o

nit rat e.

Decom posit ion rat es – m easuring t he speed of disappearance of organic residue or st andardized cot t on

st rips.
M e a sur in g ce llula r con st it u e nt s. The t ot al biom ass of all soil organism s or specific charact erist ics of t he

com m unit y can be inferred by m easuring com ponent s of soil organism s such as t he following.

Biom ass carbon, nit rogen, or phosphorus – m easure t he am ount of nut rient s in living cells, which can

t hen be used t o est im at e t he t ot al biom ass of organism s. Chloroform fum igat ion is a com m on m et hod

used t o est im at e t he am ount of carbon or nit rogen in all soil organism s.

Enzym es – m easure enzym es in living cells or at t ached t o soil. Assays can be used t o est im at e pot ent ial

act ivit y or t o charact erize t he biological com m unit y.

Phospholipids and ot her lipids – provide a “ fingerprint ” of t he com m unit y, and quant ify t he biom ass of

groups such as fungi or act inom ycet es.

DNA and RNA – provide a “ fingerprint ” of t he com m unit y, and can det ect t he presence of specific species

or groups.

W H AT I S COM PLEXI TY?

Food web com plexit y is a fact or of bot h t he num ber of species and t he num ber of different kinds of species

in t he soil. For exam ple, a soil wit h t en species of bact erial- feeding nem at odes is less com plex t han a soil

wit h t en nem at ode species t hat includes bact erial- feeders, fungal- feeders, and predat ory nem at odes.

Com plexit y can be det erm ined, in part , from a food web diagram such as Figure 4

( see diagram ) , which represent s t he soil in an old- growt h Douglas fir forest . Each box

of t he food web diagram represent s a funct ional group of organism s t hat perform

sim ilar roles in t he soil syst em . Transfers of energy are represent ed by t he arrows on

t he diagram and occur when one organism eat s anot her. Com plex ecosyst em s have

m ore funct ional groups and m ore energy t ransfers t han sim ple ecosyst em s.

The num ber of funct ional groups t hat t urn over energy before t he energy leaves t he soil syst em is different

( and charact erist ic) for each ecosyst em ( Figure 5) . I n t he Douglas fir syst em ( Figure 4) , energy m ay

undergo m ore t han t went y t ransfers from organism t o organism , or bet ween funct ional groups. I n cont rast ,

a cave or low- residue cult ivat ed syst em is not likely t o include a large variet y of higher predat ors on t he

right - hand side of a soil food web diagram . Energy and nut rient s will be cycled t hrough fewer t ypes of

organism s.

Land m anagem ent pract ices can alt er t he num ber of funct ional groups – or com plexit y – in t he soil.

I nt ensively m anaged syst em s, such as cropland, have varied num bers of funct ional groups. Crop select ions,
t illage pract ices, residue m anagem ent , pest icide use, and irrigat ion alt er t he habit at for soil organism s, and

t hus alt er t he st ruct ure and com plexit y of t he food web.

BEN EFI TS OF COM PLEXI TY

Biological com plexit y of a soil syst em can affect processes such as nut rient cycling, t he form at ion of soil

st ruct ure, pest cycles, and decom posit ion rat es. Researchers have yet t o define how m uch and what kind of

food web com plexit y in m anaged ecosyst em s is opt im al for t hese soil processes.

N u t r ie n t cyclin g. When organism s consum e food, t hey creat e m ore of t heir own biom ass and t hey release

wast es. The m ost im port ant wast e for crop growt h is am m onium ( NH4+ ) . Am m onium and ot her readily

ut ilized nut rient s are quickly t aken up by ot her organism s, including plant root s. When a large variet y of

organism s are present , nut rient s m ay cycle m ore rapidly and frequent ly am ong form s t hat plant s can and

cannot use.

N u t r ie n t r et e n t ion . I n addit ion t o m ineralizing or releasing nit rogen t o plant s, t he soil food web can

im m obilize or ret ain nit rogen when plant s are not rapidly growing. Nit rogen in t he form of soil organic

m at t er and organism biom ass is less m obile and less likely t o be lost from t he root ing zone t han inorganic

nit rat e ( NO3 - ) and am m onium ( NH4 + ) .

I m pr ove d st r u ct u r e , infilt r a t ion, a n d w a t er - h olding ca pa cit y. Many soil organism s are involved in t he

form at ion and st abilit y of soil aggregat es. Bact erial act ivit y, organic m at t er, and t he chem ical propert ies of

clay part icles are responsible for creat ing m icro- aggregat es from individual soil part icles. Eart hworm s and

art hropods consum e sm all aggregat es of m ineral part icles and organic m at t er, and generat e larger fecal

pellet s coat ed wit h com pounds from t he gut . These fecal pellet s becom e part of t he soil st ruct ure. Fungal

hyphae and root hairs bind t oget her and help st abilize larger aggregat es. I m proved aggregat e st abilit y,

along wit h t he burrows of eart hworm s and art hropods, increases porosit y, wat er infilt rat ion, and wat er-

holding capacit y.

D ise a se su ppr e ssion . A com plex soil food web cont ains num erous organism s t hat can com pet e wit h

disease- causing organism s. These com pet it ors m ay prevent soil pat hogens from est ablishing on plant

surfaces, prevent pat hogens from get t ing food, feed on pat hogens, or generat e m et abolit es t hat are t oxic t o

or inhibit pat hogens.

D e gr a da t ion of pollu t a n t s. An im port ant role of soil is t o purify wat er. A com plex food web includes

organism s t hat consum e ( degrade) a wide range of pollut ant s under a wide range of environm ent al

condit ions.
Biodive r sit y. Great er food web com plexit y m eans great er biodiversit y. Biodiversit y is m easured by t he t ot al

num ber of species, as well as t he relat ive abundance of t hese species, and t he num ber of funct ional groups

of organism s.

M AN AGEM EN T AN D SOI L H EALTH

A healt hy soil effect ively support s plant growt h, prot ect s air and wat er qualit y, and ensures hum an and

anim al healt h. The physical st ruct ure, chem ical m ake- up, and biological com ponent s of t he soil t oget her

det erm ine how well a soil perform s t hese services.

I n every healt hy syst em or wat ershed, t he soil food web is crit ical t o m aj or soil funct ions including:

1. sust aining biological act ivit y, diversit y, and product ivit y;

2. regulat ing t he flow of wat er and dissolved nut rient s;

3. st oring and cycling nut rient s and ot her elem ent s; and

4. filt ering, buffering, degrading, im m obilizing and det oxifying organic and inorganic m at erials t hat are

pot ent ial pollut ant s.

The int eract ions am ong organism s enhance m any of t hese funct ions.

Successful land m anagem ent requires approaches t hat prot ect all resources, including soil, wat er, air,

plant s, anim als and hum ans. Many m anagem ent st rat egies change soil habit at s and t he food web, and alt er

soil qualit y, or t he capacit y of soil t o perform it s funct ions. Exam ples of som e pract ices t hat change t he

com plexit y and healt h of t he soil com m unit y include:

• Com pared t o a field wit h a 2- year crop rot at ion, a field wit h a 4 crops grown in rot at ion m ay have a

great er variet y of food sources ( i.e., root s and surface residue) , and t herefore is likely t o have m ore

t ypes of bact eria, fungi, and ot her organism s.

• A cleanly- t illed field wit h few veget at ed edges m ay have fewer habit at s for art hropods t han a field

broken up by grassed wat erways, t erraces, or fence rows.

• Alt hough t he effect of pest icides on soil organism s varies, high levels of pest icide use will generally

reduce food web com plexit y. An ext rem e exam ple is t he repeat ed use of m et hyl brom ide which has

been observed t o elim inat e m ost soil organism s except a few bact eria species.

TH E FOOD W EB AN D CARBON SEQUESTRATI ON

Land m anagem ent pract ices can be chosen t o increase t he am ount of carbon sequest ered as soil organic

m at t er and reduce t he am ount of CO2 , a greenhouse gas, released t o t he at m osphere.

As t he soil food web decom poses organic m at erial, it releases carbon int o t he at m osphere as CO2 or

convert s it t o a variet y of form s of soil organic m at t er. Labile or act ive fract ions of organic m at t er st ay in t he

soil for a few years. St able form s reside in t he soil for decades or hundreds of years. Physically st abilized

organic m at t er is prot ect ed inside soil aggregat es t hat soil organism s help creat e. Hum ified organic m at t er is

st able because bact eria and fungi have helped form m olecules t hat are t oo com plex and large for soil

organism s t o decom pose.

LOOKI N G FORW ARD

The funct ions of t he food web are essent ial t o plant growt h and environm ent al qualit y. Good resource

m anagem ent will int egrat e food web- enhancing st rat egies int o t he regular act ivit ies of farm s, ranches,

forest s, or in backyard gardens. Needed research will exam ine food web funct ions wit hin whole syst em s, and

will support t echnology developm ent . Technology t o assess and m aint ain t he funct ions of soil food webs will

be developed t o assist land m anagers and researchers as t hey st rive t owards soil product ivit y and

st ewardship. I n t he com ing years, we can expect progress at answering soil biology quest ions such as t he

following.

W h a t is a h ea lt h y food w e b? What m easurem ent s or observat ions can be used t o det erm ine whet her a

part icular biological com m unit y is desirable for t he int ended land use? What level of com plexit y is opt im al

for highly product ive and sust ainable crop, range or forest lands?

I s it m or e u se fu l t o cou n t spe cie s, or t ype s of or ga n ism s? The Soil Biology Prim er divides food web

organism s int o six groups. Achieving an opt im al balance of t hese groups is one approach t o m anaging t he

food web. Alt ernat ively, ident ifying t he species and com plexit y present wit hin a group m ay provide ot her

useful inform at ion about t he healt h and product ive pot ent ial of a soil.

H ow should t he biology of t he soil be m a na ge d? I n t he fut ure, land m anagers m ay be able t o m ore

precisely predict t he effect of m anagem ent decisions such as t he t im ing of t illage, t he applicat ion of a

cert ain kind of com post , or t he use of a part icular pest icide. They m ay choose pract ices wit h t he int ent of

m aking specific changes t o t he com posit ion of t he soil food web.

W h a t a r e t he cost s a n d be n e fit s of m a na ging for soil biologica l funct ions? The cost s t o achieve a

highly diverse, or com plex, soil com m unit y need t o be ident ified. These can be com pared t o t he benefit s of

biological services provided, such as nut rient cycling, disease suppression, and soil st ruct ure enhancem ent .
Ch a pt e r 3 : BACTERI A

By Elaine R. I ngham

TH E LI VI N G SOI L: BACTERI A

Bact eria are t iny, one- celled organism s – generally 4/ 100,000 of an inch wide ( 1 µm ) and som ewhat longer

in lengt h. What bact eria lack in size, t hey m ake up in num bers. A t easpoon of product ive soil generally

cont ains bet ween 100 m illion and 1 billion bact eria. That is as m uch m ass as t wo cows per acre.

Bact eria fall int o four funct ional groups. Most are decom posers t hat consum e sim ple carbon com pounds,

such as root exudat es and fresh plant lit t er. By t his process, bact eria convert energy in soil organic m at t er

int o form s useful t o t he rest of t he organism s in t he soil food web. A num ber of decom posers can break

down pest icides and pollut ant s in soil. Decom posers are especially im port ant in im m obilizing, or ret aining,

nut rient s in t heir cells, t hus prevent ing t he loss of nut rient s, such as nit rogen, from t he root ing zone.

A second group of bact eria are t he m ut ualist s t hat form part nerships wit h plant s. The m ost well- known of

t hese are t he nit rogen- fixing bact eria. The t hird group of bact eria is t he pat hogens. Bact erial pat hogens

include Xym om onas and Erwinia species, and species of Agrobact erium t hat cause gall form at ion in plant s. A

fourt h group, called lit hot rophs or chem oaut ot rophs, obt ains it s energy from com pounds of nit rogen, sulfur,

iron or hydrogen inst ead of from carbon com pounds. Som e of t hese species are im port ant t o nit rogen

cycling and degradat ion of pollut ant s.

W H AT D O BACTERI A D O?

Bact eria from all four groups perform im port ant services relat ed t o wat er dynam ics, nut rient cycling, and

disease suppression. Som e bact eria affect wat er m ovem ent by producing subst ances t hat help bind soil

part icles int o sm all aggregat es ( t hose wit h diam et ers of 1/ 10,000- 1/ 100 of an inch or 2- 200µm ) . St able

aggregat es im prove wat er infilt rat ion and t he soil’s wat er- holding abilit y. I n a diverse bact erial com m unit y,

m any organism s will com pet e wit h disease- causing organism s in root s and on aboveground surfaces of

plant s.

A FEW I M PORTAN T BACTERI A

N it r oge n- fix ing ba ct er ia form sym biot ic associat ions wit h t he root s of legum es like clover and lupine, and

t rees such as alder and locust . Visible nodules are creat ed where bact eria infect a growing root hair ( Figure

4) . The plant supplies sim ple carbon com pounds t o t he bact eria, and t he bact eria convert nit rogen ( N2)
from air int o a form t he plant host can use. When leaves or root s from t he host plant decom pose, soil

nit rogen increases in t he surrounding area.

N it r ifying ba ct e r ia change am m onium ( NH4+ ) t o nit rit e ( NO2- ) t hen t o nit rat e ( NO3- ) – a preferred form

of nit rogen for grasses and m ost row crops. Nit rat e is leached m ore easily from t he soil, so som e farm ers

use nit rificat ion inhibit ors t o reduce t he act ivit y of one t ype of nit rifying bact eria. Nit rifying bact eria are

suppressed in forest soils, so t hat m ost of t he nit rogen rem ains as am m onium .

D e n it r ifyin g ba ct er ia convert nit rat e t o nit rogen ( N2) or nit rous oxide ( N2O) gas. Denit rifiers are

anaerobic, m eaning t hey are act ive where oxygen is absent , such as in sat urat ed soils or inside soil

aggregat es.

Act inom yce t e s are a large group of bact eria t hat grow as hyphae like fungi ( Figure 3) . They are

responsible for t he charact erist ically “ eart hy” sm ell of freshly t urned, healt hy soil. Act inom ycet es decom pose

a wide array of subst rat es, but are especially im port ant in degrading recalcit rant ( hard- t o- decom pose)

com pounds, such as chit in and cellulose, and are act ive at high pH levels. Fungi are m ore im port ant in

degrading t hese com pounds at low pH. A num ber of ant ibiot ics are produced by act inom ycet es such as

St rept om yces.

W H ERE ARE BACTERI A?

Various species of bact eria t hrive on different food sources and in different m icroenvironm ent s. I n general,

bact eria are m ore com pet it ive when labile ( easy- t o- m et abolize) subst rat es are present . This includes fresh,

young plant residue and t he com pounds found near living root s. Bact eria are especially concent rat ed in t he

rhizosphere, t he narrow region next t o and in t he root . There is evidence t hat plant s produce cert ain t ypes

of root exudat es t o encourage t he growt h of prot ect ive bact eria.

Bact eria alt er t he soil environm ent t o t he ext ent t hat t he soil environm ent will favor cert ain plant

com m unit ies over ot hers. Before plant s can becom e est ablished on fresh sedim ent s, t he bact erial

com m unit y m ust est ablish first , st art ing wit h phot osynt het ic bact eria. These fix at m ospheric nit rogen and

carbon, produce organic m at t er, and im m obilize enough nit rogen and ot her nut rient s t o init iat e nit rogen

cycling processes in t he young soil. Then, early successional plant species can grow. As t he plant com m unit y

is est ablished, different t ypes of organic m at t er ent er t he soil and change t he t ype of food available t o

bact eria. I n t urn, t he alt ered bact erial com m unit y changes soil st ruct ure and t he environm ent for plant s.
Som e researchers t hink it m ay be possible t o cont rol t he plant species in a place by m anaging t he soil

bact eria com m unit y.

BUG BI OGRAPH Y: Ba ct e r ia Th a t Pr om ot e Pla n t Gr ow t h

By Ann Kennedy, USDA Agricult ural Research Service, Pullm an, WA

Cert ain st rains of t he soil bact eria Pseudom onas fluorescens have ant i- fungal act ivit y t hat inhibit s som e

plant pat hogens. P. fluorescens and ot her Pseudom onas and Xant hom onas species can increase plant

growt h in several ways. They m ay produce a com pound t hat inhibit s t he growt h of pat hogens or reduces

invasion of t he plant by a pat hogen. They m ay also produce com pounds ( growt h fact ors) t hat direct ly

increase plant growt h.

These plant growt h- enhancing bact eria occur nat urally in soils, but not always in high enough num bers t o

have a dram at ic effect . I n t he fut ure, farm ers m ay be able t o inoculat e seeds wit h ant i- fungal bact eria, such

as P. fluorescens, t o ensure t hat t he bact eria reduce pat hogens around t he seed and root of t he crop.

Ch a pt e r 4 : SOI L FUN GI

By Elaine R. I ngham

TH E LI VI N G SOI L: FUN GI

Fungi are m icroscopic cells t hat usually grow as long t hreads or st rands called hyphae, which push t heir way

bet ween soil part icles, root s, and rocks. Hyphae are usually only several t housandt hs of an inch ( a few

m icrom et ers) in diam et er. A single hyphae can span in lengt h from a few cells t o m any yards. A few fungi,

such as yeast , are single cells.

Hyphae som et im es group int o m asses called m ycelium or t hick, cord- like “ rhizom orphs” t hat look like root s.

Fungal fruit ing st ruct ures ( m ushroom s) are m ade of hyphal st rands, spores, and som e special st ruct ures like

gills on which spores form . ( See figure) A single individual fungus can include m any fruit ing bodies scat t ered

across an area as large as a baseball diam ond.

Fungi perform im port ant services relat ed t o wat er dynam ics, nut rient cycling, and disease suppression.

Along wit h bact eria, fungi are im port ant as decom posers in t he soil food web. They convert hard- t o- digest

organic m at erial int o form s t hat ot her organism s can use. Fungal hyphae physically bind soil part icles

t oget her, creat ing st able aggregat es t hat help increase wat er infilt rat ion and soil wat er holding capacit y.
Soil fungi can be grouped int o t hree general funct ional groups based on how t hey get t heir energy.

Decom posers – saprophyt ic fungi – convert dead organic m at erial int o fungal biom ass, carbon dioxide

( CO2) , and sm all m olecules, such as organic acids. These fungi generally use com plex subst rat es, such as

t he cellulose and lignin, in wood, and are essent ial in decom posing t he carbon ring st ruct ures in som e

pollut ant s. A few fungi are called “ sugar fungi” because t hey use t he sam e sim ple subst rat es as do m any

bact eria. Like bact eria, fungi are im port ant for im m obilizing, or ret aining, nut rient s in t he soil. I n addit ion,

m any of t he secondary m et abolit es of fungi are organic acids, so t hey help increase t he accum ulat ion of

hum ic- acid rich organic m at t er t hat is resist ant t o degradat ion and m ay st ay in t he soil for hundreds of

years.

Mut ualist s – t he m ycorrhizal fungi – colonize plant root s. I n exchange for carbon from t he plant , m ycorrhizal

fungi help solubolize phosphorus and bring soil nut rient s ( phosphorus, nit rogen, m icronut rient s, and perhaps

wat er) t o t he plant . One m aj or group of m ycorrhizae, t he ect om ycorrhizae ( Figure 3) , grow on t he surface

layers of t he root s and are com m only associat ed wit h t rees. The second m aj or group of m ycorrhizae are t he

endom ycorrhizae t hat grow wit hin t he root cells and are com m only associat ed wit h grasses, row crops,

veget ables, and shrubs. Arbuscular m ycorrhizal ( AM) fungi ( Figure 4) are a t ype of endom ycorrhizal fungi.

Ericoid m ycorrhizal fungi can by eit her ect o- or endom ycorrhizal.

The t hird group of fungi, pat hogens or parasit es, cause reduced product ion or deat h when t hey colonize

root s and ot her organism s. Root - pat hogenic fungi, such as Vert icillium , Pyt hium , and Rhizoct onia, cause

m aj or econom ic losses in agricult ure each year. Many fungi help cont rol diseases. For exam ple, nem at ode-

t rapping fungi t hat parasit ize disease- causing nem at odes, and fungi t hat feed on insect s m ay be useful as

biocont rol agent s.

WHERE ARE FUNGI ?

Saprophyt ic fungi are com m only act ive around woody plant residue. Fungal hyphae have advant ages over

bact eria in som e soil environm ent s. Under dry condit ions, fungi can bridge gaps bet ween pocket s of

m oist ure and cont inue t o survive and grow, even when soil m oist ure is t oo low for m ost bact eria t o be

act ive. Fungi are able t o use nit rogen up from t he soil, allowing t hem t o decom pose surface residue which is

oft en low in nit rogen.

Fungi are aerobic organism s. Soil which becom es anaerobic for significant periods generally loses it s fungal

com ponent . Anaerobic condit ions oft en occur in wat erlogged soil and in com pact ed soils.
Fungi are especially ext ensive in forest ed lands. Forests have been observed t o increase in product ivit y as

fungal biom ass increases.

M YCORRH I ZAL FUN GI I N AGRI CULTURE

Mycorrhiza is a sym biot ic associat ion bet ween fungi and plant root s and is unlike eit her fungi or root s alone.

Most t rees and agricult ural crops depend on or benefit subst ant ially from m ycorrhizae. The except ions are

m any m em bers of t he Cruciferae fam ily ( e.g., broccoli, m ust ard) , and t he Chenopodiaceae fam ily ( e.g.

lam bsquart ers, spinach, beet s) , which do not form m ycorrhizal associat ions. The level of dependency on

m ycorrhizae varies great ly am ong variet ies of som e crops, including wheat and corn.

Land m anagem ent pract ices affect t he form at ion of m ycorrhizae. The num ber of m ycorrhizal fungi in soil will

decline in fallowed fields or in t hose plant ed t o crops t hat do not form m ycorrhizae. Frequent t illage m ay

reduce m ycorrhizal associat ions, and broad spect rum fungicides are t oxic t o m ycorrhizal fungi. Very high

levels of nit rogen or phosphorus fert ilizer m ay reduce inoculat ion of root s. Som e inoculum s of m ycorrhizal

fungi are com m ercially available and can be added t o t he soil at plant ing t im e.

Ch a pt e r 5 : SOI L PROTOZOA

By Elaine R. I ngham

TH E LI VI N G SOI L: PROTOZOA

Prot ozoa are single- celled anim als t hat feed prim arily on bact eria, but also eat ot her prot ozoa, soluble

organic m at t er, and som et im es fungi. They are several t im es larger t han bact eria – ranging from 1/ 5000 t o

1/ 50 of an inch ( 5 t o 500 µm ) in diam et er. As t hey eat bact eria, prot ozoa release excess nit rogen t hat can

t hen be used by plant s and ot her m em bers of t he food web.

Prot ozoa are classified int o t hree groups based on t heir shape: Ciliat es are t he largest and m ove by m eans

of hair- like cilia. They eat t he ot her t wo t ypes of prot ozoa, as well as bact eria. Am oebae also can be quit e

large and m ove by m eans of a t em porary foot or “ pseudopod.” Am oebae are furt her divided int o t est at e

am oebae ( which m ake a shell- like covering) and naked am oebae ( wit hout a covering) . Flagellat es are t he

sm allest of t he prot ozoa and use a few whip- like flagella t o m ove.
W H AT D O PROTOZOA D O?

Prot ozoa play an im port ant role in m ineralizing nut rient s, m aking t hem

available for use by plant s and ot her soil organism s. Prot ozoa ( and

nem at odes) have a lower concent rat ion of nit rogen in t heir cells t han t he

bact eria t hey eat . ( The rat io of carbon t o nit rogen for prot ozoa is 10: 1 or

m uch m ore and 3: 1 t o 10: 1 for bact eria.) Bact eria eat en by prot ozoa

cont ain t oo m uch nit rogen for t he am ount of carbon prot ozoa need. They release t he excess nit rogen in t he

form of am m onium ( NH4+ ) . This usually occurs near t he root syst em of a plant . Bact eria and ot her

organism s rapidly t ake up m ost of t he am m onium , but som e is used by t he plant . ( See figure for

explanat ion of m ineralizat ion and im m obilzat ion.)

Anot her role t hat prot ozoa play is in regulat ing bact eria populat ions. When t hey graze on bact eria, prot ozoa

st im ulat e growt h of t he bact erial populat ion ( and, in t urn, decom posit ion rat es and soil aggregat ion.)

Exact ly why t his happens is under som e debat e, but grazing can be t hought of like pruning a t ree – a sm all

am ount enhances growt h, t oo m uch reduces growt h or will m odify t he m ix of species in t he bact erial

com m unit y.

Prot ozoa are also an im port ant food source for other soil organism s and help t o suppress disease by

com pet ing wit h or feeding on pat hogens.

W H ERE ARE PROTOZOA?

Prot ozoa need bact eria t o eat and wat er in which t o m ove, so m oist ure plays a big role in det erm ining which

t ypes of prot ozoa will be present and act ive. Like bact eria, prot ozoa are part icularly act ive in t he rhizosphere

next t o root s.

Typical num bers of prot ozoa in soil vary widely – from a t housand per t easpoon in low fert ilit y soils t o a

m illion per t easpoon in som e highly fert ile soils. Fungal- dom inat ed soils ( e.g. forest s) t end t o have m ore

t est at e am oebae and ciliat es t han ot her t ypes. I n bact erial- dom inat ed soils, flagellat es and naked am oebae

predom inat e. I n general, high clay- cont ent soils cont ain a higher num ber of sm aller prot ozoa ( flagellat es

and naked am oebae) , while coarser t ext ured soils cont ain m ore large flagellat es, am oebae of bot h variet ies,

and ciliat es.

N EM ATOD ES AN D PROTOZOA

Prot ozoa and bact erial- feeding nem at odes com pet e for t heir com m on food resource: bact eria. Som e soils

have high num bers of eit her nem at odes or prot ozoa, but not bot h. The significance of t his difference t o

plant s is not known. Bot h groups consum e bact eria and release NH4+ .

BUG BI OGRAPH Y: Soil D w e llin g Va m pir e s

Most prot ozoa eat bact eria, but one group of am oebae, t he vam pyrellids, eat

fungi. The perfect ly round holes drilled t hrough t he fungal cell wall, m uch like t he

purport ed punct ure m arks on t he neck of a vam pire’s vict im , are evidence of t he

presence of vam pyrellid am oebae. The am oebae at t ach t o t he surface of fungal

hyphae and generat e enzym es t hat eat t hrough t he fungal cell wall. The am oeba

t hen sucks dry or engulfs t he cyt oplasm inside t he fungal cell before m oving on t o

it s next vict im .

Vam pyrellids at t ack m any fungi including root pat hogens, such as Gaeum annom yces gram inis, shown in t he

phot o. This fungus at t acks wheat root s and causes t ake- all disease.

Ch a pt e r 6 : N EM ATOD ES

By Elaine R. I ngham

TH E LI VI N G SOI L: N EM ATOD ES

Nem at odes are non- segm ent ed worm s t ypically 1/ 500 of an inch ( 50 µm ) in diam et er and 1/ 20 of an inch ( 1

m m ) in lengt h. Those few species responsible for plant diseases have received a lot of at t ent ion, but far less

is known about t he m aj orit y of t he nem at ode com m unit y t hat plays beneficial roles in soil.

An incredible variet y of nem at odes funct ion at several t rophic levels of t he soil food web. Som e feed on t he

plant s and algae ( first t rophic level) ; ot hers are grazers t hat feed on bact eria and fungi ( second t rophic

level) ; and som e feed on ot her nem at odes ( higher t rophic levels) .

Free- living nem at odes can be divided int o four broad groups based on t heir diet . Bact erial- feeders consum e

bact eria. Fungal- feeders feed by punct uring t he cell wall of fungi and sucking out t he int ernal cont ent s.

Predat ory nem at odes eat all t ypes of nem at odes and prot ozoa. They eat sm aller organism s whole, or at t ach

t hem selves t o t he cut icle of larger nem at odes, scraping away unt il t he prey’s int ernal body part s can be
ext ract ed. Om nivores eat a variet y of organism s or m ay have a different diet at each life st age. Root - feeders

are plant parasit es, and t hus are not free- living in t he soil.

W H AT D O N EM ATOD ES D O?

N u t r ie n t cyclin g. Like prot ozoa, nem at odes are im port ant in m ineralizing, or releasing, nut rient s in plant -

available form s. When nem at odes eat bact eria or fungi, am m onium ( NH4+ ) is released because bact eria

and fungi cont ain m uch m ore nit rogen t han t he nem at odes require.

Gr a zin g. At low nem at ode densit ies, feeding by nem at odes st im ulat es t he growt h rat e of prey populat ions.

That is, bact erial- feeders st im ulat e bact erial growt h, plant - feeders st im ulat e plant growt h, and so on. At

higher densit ies, nem at odes will reduce t he populat ion of t heir prey. This m ay decrease plant product ivit y,

m ay negat ively im pact m ycorrhizal fungi, and can reduce decom posit ion and im m obilizat ion rat es by

bact eria and fungi. Predat ory nem at odes m ay regulat e populat ions of bact erial- and fungal- feeding

nem at odes, t hus prevent ing over- grazing by t hose groups. Nem at ode grazing m ay cont rol t he balance

bet ween bact eria and fungi, and t he species com posit ion of t he m icrobial com m unit y.

D ispe r sa l of m icr obe s. Nem at odes help dist ribut e bact eria and fungi t hrough t he soil and along root s by

carrying live and dorm ant m icrobes on t heir surfaces and in t heir digest ive syst em s.

Food sour ce . Nem at odes are food for higher level predat ors, including predat ory nem at odes, soil

m icroart hropods, and soil insect s. They are also parasit ized by bact eria and fungi.

D ise a se su ppr e ssion a n d de ve lopm e nt . Som e nem at odes cause disease. Ot hers consum e disease-

causing organism s, such as root - feeding nem at odes, or prevent t heir access t o root s. These m ay be

pot ent ial biocont rol agent s.

W H ERE ARE N EM ATOD ES?

Nem at odes are concent rat ed near t heir prey groups. Bact erial- feeders abound near root s where bact eria

congregat e; fungal- feeders are near fungal biom ass; root - feeders are concent rat ed around root s of st ressed

or suscept ible plant s. Predat ory nem at odes are m ore likely t o be abundant in soils wit h high num bers of

nem at odes.
Because of t heir size, nem at odes t end t o be m ore com m on in coarser- t ext ured soils. Nem at odes m ove in

wat er film s in large ( > 1/ 500 inch or 50 µm ) pore spaces.

Agricult ural soils generally support less t han 100 nem at odes in each t easpoon ( dry gram ) of soil. Grasslands

m ay cont ain 50 t o 500 nem at odes, and forest soils generally hold several hundred per t easpoon. The

proport ion of bact erial- feeding and fungal- feeding nem at odes is relat ed t o t he am ount of bact eria and fungi

in t he soil. Com m only, less dist urbed soils cont ain m ore predat ory nem at odes, suggest ing t hat predat ory

nem at odes are highly sensit ive t o a wide range of dist urbances.

N EM ATOD ES AN D SOI L QUALI TY

Nem at odes m ay be useful indicat ors of soil quality because of t heir t rem endous diversit y and t heir

part icipat ion in m any funct ions at different levels of t he soil food web. Several researchers have proposed

approaches t o assessing t he st at us of soil qualit y by count ing t he num ber of nem at odes in different fam ilies

or t rophic groups.* I n addit ion t o t heir diversit y, nem at odes m ay be useful indicat ors because t heir

populat ions are relat ively st able in response t o changes in m oist ure and t em perat ure ( in cont rast t o

bact eria) , yet nem at ode populat ions respond t o land m anagem ent changes in predict able ways. Because

t hey are quit e sm all and live in wat er film s, changes in nem at ode populat ions reflect changes in soil

m icroenvironm ent s.

* Blair, J. M. et al. 1996. Soil invert ebrat es as indicat ors of soil qualit y. I n Met hods for Assessing Soil Qualit y,

SSSA Special Publicat ion 49, pp. 273- 291.

BUG BI OGRAPH Y: N e m a t ode Tr a ppe r s

One group of fungi m ay be a useful biological cont rol agent against parasit ic nem at odes. These predat ory

fungi grow t hrough t he soil, set t ing out t raps when t hey det ect signs of t heir prey. Som e species use st icky

t raps, ot hers m ake circular rings of hyphae t o const rict t heir prey. When t he t rap is set , t he fungi put out a

lure, at t ract ing nem at odes t hat are looking for lunch. The nem at ode, however, becom es lunch for t he

fungus.
REFEREN CES:

Soil Biology Prim er [ online] . Available: soils.usda.gov/ sqi/ concept s/ soil_biology/ biology.ht m l [ access dat e] .

Eit her of t he following are correct cit at ions for t he current edit ion of t he booklet :

Tugel, Arlene, Ann Lewandowski, Deb Happe- vonArb, eds. 2000. Soil Biology Prim er. Rev. ed. Ankeny,

I owa: Soil and Wat er Conservat ion Societ y.

Soil and Wat er Conservat ion Societ y ( SWCS) . 2000. Soil Biology Prim er. Rev. ed. Ankeny, I owa: Soil and

Wat er Conservat ion Societ y.

Cit at ion for t he first edit ion of t he booklet :

Tugel, A.J., A.M. Lewandowski, eds. 1999. Soil Biology Prim er. NRCS Soil Qualit y I nst it ut e, Am es, I A.

Ack n ow le dge m e n t s

The form er Soil Qualit y I nst it ut e of t he Nat ural Resources Conservat ion Service, wit h assist ance from t he

Conservat ion Technology I nform at ion Cent er, provided leadership for t his proj ect . The Nat ural Resources

Conservat ion Service and t he Soil and Wat er Conservat ion Societ y t hank m any individuals, including t he

following, for t heir cont ribut ions.