O. R. S.T. O. 1% torias Documentai@

CHAPTER 35

MICROBIAL ACTIVITY IN DIFFERENT TYPES OF MICROENVIRONMENTS IN PADDY SOILS

Y . DOMMERGUES

Centre de PQdologie Biologique du CNRS B.P. 5 - 54500 Vandoeuvre-les-Nancy, France

Orstom - B. P. 1386 - Dakar, Senegal

GENERAL CHARACTERISTICS OF PADDY SOILS

Most s t u d i e s on paddy s o i l s have h i t h e r t o been con- cerned by t h e o v e r a l l e f f e c t of submergence on b i o l o g i c a l and chemical s o i l p rope r t i e s (Redman and Pa t r i ck , 1965; Turner and P a t r i c k , 1968). The sequence of oxido-reduction changes i n s o i l s t h a t occur as a r e s u l t of waterlogging together with t ransformation of manganese from the e a s i l y reducib le form t o t h e exchangeable form (Mn*), reduct ion of Fe, release of phosphorus from t h e non ex t r ac t ab le t o t h e ex t r ac t ab le form and eventua l ly formation of S', H2, CH4 has been s tudied by d i f f e r e n t authors . Figure 1 is a classical example of t h e e f f e c t of waterlogging on some chemical c h a r a c t e r i s t i c s of a s o i l .

' I n an exce l l en t review, Yoshida (1975) c l e a r l y empha- s i zed t h e classical time sequence of t h e opera t ions usua l ly performed i n paddy f i e l d s : (1) submergence of t h e s o i l , wi th o r without puddling, f o r t he dura t ion of t h e crop, wi th o r without s o i l drying i n midseason, (2) dra in ing and drying t h e s o i l s before ha rves t , and (3) ref looding f o r t h e next crop a few weeks t o seve ra l months a f t e r harves t . quoted by Yoshida (1975), s tud ied t h e success ive reducing pro- cesses t h a t occurred a f t e r t h e submergence (Table I ) .

paddy s o i l s , even i n t h e submergence phase, are f a r from being uniformly a t a given reducing level. regarded as complex systems formed up by t h e jux tapos i t i on of microenvironments which are e i t h e r si tes of ox ida t ion re- ac t ions o r sites of reduct ion r eac t ions mediated by a h o s t s o i l microorganisms. This chapter w i l l p resent t h e d i f f e r e n t ca t egor i e s of environments occurr ing i n paddy @&i&,.so T. am &g,

Takai e t aZ.,

Actual ly , it has not been s u f f i c i e n t l y emphasized t h a t

Paddy s o i l s should be

JbllM 3979

451

452 The TerrestriaZ Environment

Time after waterlogging (Days)

Figure 1. Changes i n oxygen, n i t r a t e , manganese, i r o n and redox p o t e n t i a l i n a s i l t y c lay as a r e s u l t of waterlogging (Turner and P a t r i c k , 1968).

Table I Successive Microbial Reduction Processes

i n Flooded Soi l sa

Transformation Biochemical of Elements I n i t i a l S o i l Eh P a t t e r n

Disappearance of NO-3 Disappearance of NO3 Formation of Mn2+ Formation of Fe2+ Formation of S2- Formation of H2 Formation of CH4

+ 0.6 % + 0.5 + 0.6 % + 0.5 + 0.6 % + 0.4 + 0.6 + 0.3

o 'L - 0.19 - 0.15%- 0.22 - 0.15%- 0.19

Aerobic r e s p i r a t i o n Anaerobic r e s p i r a t i o n Anaerobic r e s p i r a t i o n Anaerobic r e s p i r a t i o n Anaerobic r e s p i r a t i o n Fermentation Fermentation

aYoshida, 1975.

MICROBIAL ACTIVITIES I N LARGER MICROENVIRONMENTS

Three l a y e r s are usua l ly repor ted i n a submerged paddy s o i l (Figure 2 ) . These are t h e l i q u i d l aye r ( f lood water), t h e aerobic s o i l l aye r and aerobic-anaerobic i n t e r f a c e , and t h e anaerobic s o i l l ayer . Aquatic p l a n t s and r ice are

Y2

Paddy SoiZs, Peat, CoaZ 453

Shallow Floodwater

Aerobic Soil Layer

Aerobic - Anaerobic interface

Anaerobic Soil Layer

Figure 2. Schematic representation of a paddy soil profile indicating the existence of differents layers: water, aerobic and aerobic-anaerobic interface, anaerobic layer (Reddy e t aZ., 1976).

flood

454 The Terrestria2 Environment

respons ib le f o r t h e occurrence of a t least two more micro- environments i n t h e so-cal led anaerobic s o i l l aye r : p l an t rhizosphere microenvironment and t h e roo t l i t t e r and s tubble environment.

Flood Water Environment

t h e

Microorganisms are present i n l a r g e numbers i n t h e water l a y e r of paddy f i e l d s . Among them, a lgae together with aqua t i c weeds, p lay a prominent r o l e by supplying oxygen through photosynthesis. i n t h e water l aye r are w e l l known and are respons ib le f o r v a r i a t i o n s i n t h e oxidat ion-reduct ion equi l ibr ium of t h é water l aye r i t s e l f and a l s o of t h e soi l -water i n t e r f ace . The concentrat ion of dissolved O2 w a s reported t o vary from 2 t o 18 ppm (Yoshida, 1975).

The r o l e of a lgae i n t h e water l aye r , e spec ia l ly as N2-fixing organisms, w a s s tud ied ex tens ive ly by Venkataraman (1975) i n A s i a and r ecen t ly by Reynaud and Roger (1977) i n

Western Afr ica . Watanabe et aZ., (1977) showed t h a t when rep lac ing f looding water and f l o a t i n g a l g a l mass with d is - t i l l e d water, in situ N2 f i x a t i o n (C2H2-C2H4) w a s d ramat ica l ly reduced i n IRRI's paddy f i e l d s from 117 t o 19 mol when a lgae bloomed. A t a later s t age , t h e removal of a lgae from f looding water d id not in f luence in situ N2 f i x a t i o n of t h e paddy s o i l . Reynaud and Roger (1977) repor ted t h a t , i n Senegal, growth and N2-fixing a c t i v i t y of blue-green a lgae were dependent upon t h e r ice p l a n t cover. A t e a r l y s t ages , N2-fixing a c t i v i t y w a s low, due t o t h e inh ib i to ry e f f e c t of h igh l i g h t i n t e n s i t y (70,000 lux a t 1:00 pm). Later, however, when t h e r ice leaves pro tec ted t h e water l aye r aga ins t excessive l i g h t , blue-green a lgae could p r o l i f e r - a te and f i x N 2 ac t ive ly . c o n s t i t u t e a favorable environment f o r N2 f i x a t i o n , bu t ex- t e r n a l changes (e.g., l i g h t i n t e n s i t y ) may alter t h i s charac te r is t ic.

Diurnal v a r i a t i o n s i n oxygen dissolved

mol C2Hq per 24 h r

1

Thus t h e water l a y e r appears t o

The Aerobic S o i l Layer

A t h i n oxidized l a y e r develops i n t h e upper p a r t of t h e paddy s o i l . Aerobic processes , such as n i t r i f i c a t i o n , are known t o take place i n t h i s horizon (Greene, 1960). Simultaneously d e n i t r i f i c a t i o n and ammonification may occur i n lower horizons, causing l a r g e l o s s e s of N2.

The Anaerobic S o i l Layer

The horizon placed beneath t h e aerobic s o i l l aye r is anaerobic and more o r less reduced. This horizon i s the s i t e of anaerobic processes

Paddy SoiZs, Peat, CoaZ 455 i -

r The Anaerobic S o i l Layer

The horizon placed beneath the aerobic s o i l l aye r i s anaerobic and more o r less reduced. This horizon is t h e si te of anaerobic processes , b u t , cont ra ry t o t h e often-held b e l i e f , such processes occur only i n favorable microenvironments, e spec ia l ly i n sites of accumulation of roo t l i t ter o r s tubble .

The Rhizosphere Microenvironment

It has long been known t h a t t h e microbial populat ion and microbial a c t i v i t y i n t h e rhizosphere d i f f e r s markedly from t h a t occurr ing i n t h e s o i l i t s e l f . f a c e area of p l a n t r o o t s is much l a r g e r than t h e s o i l sur- f a c e occupied by t h e p l a n t s , one can e a s i l y p red ic t t h a t t h e rhizosphere environment should p lay a major r o l e i n t h e biology of paddy s o i l s . I n t h e r o o t environment rice p l a n t s g r e a t l y inf luence d i f f e r e n t microbia l act ivi t ies , e spec ia l ly N, f i x a t i o n , d e n i t r i f i c a t i o n , s u l f a t e reduct ion , methane product ion.

i t s a b i l i t y t o f a c i l i t a t e t h e t r a n s f e r of oxygen from t h e f o l i a g e t o t h e rhizosphere (Ishizuka, 1971; Luxmoore e t aZ., 1970). Recent tracer s t u d i e s showed t h a t i n t h e rice rhizo- sphere t h e relative p a r t i a l p ressure w a s s t i l l 0.2 f o r 40-cm long r o o t s , whereas the correspondin ba r l ey w a s n i l (Figure 3 ) . Using a f 5 N tracer technique,

Since the t o t a l sur-

Among t h e unique c h a r a c t e r i s t i c s of t h e r ice roo t is

pressure f o r corn and

\ 0.2

CORN

L 1 - I I -, I I I I

O 5 10 15 20 25 30 35 4

Figure 3. Relative p a r t i a l p ressure of oxygen a t t h e r o o t t i p as a func t ion of t h e r o o t l eng th (L) (Jensen et aZ., 1967).

456 The Terrestr ial Environment ~

Yoshida and Broadbent (1975) confirmed t h a t a similar t rans- f e r occurred f o r atmospheric ni t rogen. A t t h e t i l l e r i n g s t a g e , t h e rate of atmospheric n i t rogen d i f f u s i o n through the p l a n t appeared t o slow down, whereas t h i s rate w a s much g rea t e r a t t h e heading o r flowering s tage . around t h e rice roo t d i f f e r markedly from those observed around p l a n t s growing i n drained s o i l s .

Thus p02, pN2, pC02 g rad ien t s

N2 Fixation

Rice r o o t s harbor d iazot rophic b a c t e r i a belonging t o t h e fol lowing genera: Beijerinckia, FZavobacteriwn, Arthrobacter, BaciZZus, Clostr i - d i m , SpiriZZwn, Enterobacter (Balandreau e t al.. , 1976; Yoshida, 1970). Most of t h e s e b a c t e r i a are microaerophi l ic ; anaerobic b a c t e r i a are less abundant (Table 11).

Pseudomonas, Azotomonas, Azotobacter,

Table II MPN Counts ( i n b a c t e r i a l g of dry s o i l ) of N2-Fixing i n t h e Rice Rhizospherea

Microaerophi l ic Anaerobic

Nonrhizosphere s o i l (cont ro l ) 3,200,000 372,000 Rhizosphere s o i l 21,900,000 1,350,000 Rhizosphere s o i l + r o o t s 61,500,000 472,600

aBalandreau e t a l . , 1976.

I n paddy f i e l d s , rhizosphere b a c t e r i a toge ther wi th nonrhizosphere diazotrophs con t r ibu te t o N2 f ixa t ion : (1) blue-green a lgae , (2) nonsymbiotic saprophyt ic N2-fixing b a c t e r i a u t i l i z i n g organic r e s idues , e spec ia l ly t h e roo t l i t t e r , and (3) a water f e rn , AzoZZa, assoc ia t ed with a blue-green a lgae (Anabaena azoZZae) . N2 f i x a t i o n through rhizosphere b a c t e r i a i s d i f f i c u l t t o measure i n situ because of t he in t e r f e rence of t h e o ther diazotrophs. However, l abora tory experiments show c l e a r l y t h a t , i n t h e absence of blue-green algae, N2 f i x a t i o n is loca ted i n t h e r o o t microenvironment (Haucke-Pacewiczowa e t a l . , 1970).

Denitrif {cation

According t o Woldendorp (1963a, b) d e n i t r i f i c a t i o n i n t h e rhizosphere of grasses accounts f o r l o s s e s of 15-37 percent of f e r t i l i z e r n i t rogen added t o t h e s o i l . This rhizosphere phenomenon who showed t h a t t h e rhizosphere s o i l exhib i ted a c t u a l and p o t e n t i a l d e n i t r i f i c a t i o n rates up t o four times those of t h e nonrhizosphere s o i l (Figure 4) . Exudates

Paddy SoiZs, Peat, Coa2 457

I I I 50 100 150 Hours

0 o (R) rhizosphere O (s) non rhizosphere soil

Figure 4. P o t e n t i a l d e n i t r i f i c a t i o n measured as N2 evolved innonrhizosphere and r ice rhizosphere s o i l (Garcia, 1973a).

are obviously used by d e n i t r i f y i n g b a c t e r i a as a source of e lec t rons . t o vary from 1 t o 514, depending on t h e s o i l type (Garcia, 1973).

ca t ion . However, t h e p o s s i b i l i t y of d e n i t r i f i c a t i o n i n two o the r environments must no t be overlooked: decaying crop r e s idues , which act as source of e l ec t rons f o r he t e ro t roph ic d e n i t r i f i e r s and sites containing s u l f i d e o r hydrogen, which are used as e l e c t r o n donors by ThiobaciZZus denitrifieans and Micrococcus denitri f ieans, respec t ive ly .

Sulfate Reduction

RIS r a t i o s of d e n i t r i f y i n g b a c t e r i a were repor ted

Thus rhizosphere is a p r e f e r e n t i a l s i t e f o r d e n i t r i f i -

I n s p i t e of t h e f a c t t h a t oxygen can d i f f u s e i n t h e near rhizosphere, s u l f a t e reduct ion may be observed i n t h e r o o t zone, provided t h a t t h e s u l f a t e content of t he s o i l is h igh enough (Jacq, 1972; Garcia e t aZ., 1974). Closer

458 The Terrestriai? Environment

i nves t iga t ions r ecen t ly showed t h a t , cont ra ry t o diazotrophs, sulfate-reducing b a c t e r i a were not loca ted i n the endorhizo- sphere1 bu t were th r iv ing i n the rhizoplane (Table I I I ) .

Such a conclusion r e s u l t e d from t h e comparison of two sets of rice roots . Roots of t h e f i r s t set were thoroughly washed wi th steri le water, thus e l imina t ing rhizoplane b a c t e r i a bu t unaf fec t ing endorhizosphere bac te r i a . Roots of t he second set were su r face s t e r i l i z e d by a 1 percent chloramine T solu- t i o n t h a t k i l l e d rhizoplane bac te r i a . N o s u l f a t e b a c t e r i a could surv ive the su r face s t e r i l i z a t i o n t reatment , i nd ica t ing t h a t they were not loca ted i n the endorhizosphere and thus were not pro tec ted a g a i n s t t h e s t e r i l i z i n g agent, un l ike d i - azotrophs (Hamad-Fares e t ai?. , 1978).

Methane Production

I n Senegalese paddy s o i l s , micropopulation of 105-107 (per g) methane-producing b a c t e r i a were reported by Garcia e t ai?. (1974); populat ion s i z e s i n r ice rhizosphere are unknown. Raimbault (personal communication) showed t h a t methane evoluat ion w a s 6-12 t i m e s h igher i n t h e r ice rhizo- sphere compared with t h e con t ro l without p lan t . These d a t a provide f u r t h e r evidence of t h e ex is tence of an anaerobic microhabi ta t i n t he rice rhizosphere, which is probably loca ted ou t s ide the endorhizosphere.

Root L i t t e r and Stubble Environment .J

A considerable propor t ion of t h e p l an t biomass is i n the form of r o o t s , which are progress ive ly subjected t o decay. I n s p i t e of t h e f a c t t h a t information colncerning roo t decomposition is st i l l scarce (Waid, 1974), one may assume t h a t t h e input of energy i n t o t h e s o i l through decay- ing r o o t s (rhizo-deposition) p lays a prominent r o l e through sus t a in ing t h e d i f f e r e n t microbia l act ivi t ies a t the si tes of decomposition.

f i e l d s should be a t t r i b u t e d t o diazotrophs assoc ia ted w i t h decaying rice roots . Rice s tubb le , which is o f t e n ploughed i n t o t h e s o i l , may'also be a favorable environment of N2 f ixa t ion . Thus Watanabe e t aZ., (1977) found r ecen t ly t h a t

'Typically, t he rhizosphere can be divided i n t o t h r e e

Probably p a r t of in situ N2 f i x a t i o n measured i n paddy

areas: comprising t h e reg ion of t h e s o i l immediately surrounding 'the p l an t r o o t s and the micropopulations l i v i n g i n t h i s zone; (2) t h e rh izoplane (= r o o t . s u r f a c e ) formed by t h e r o o t su r f ace and t h e microorganisms l i v i n g on it; (3) t h e endorhizosphere (= inner rhizosphere) formed by t h e r o o t c o r t i c a l o f t en moribund t i s s u e invaded and colonized by saprophyt ic s o i l microorganisms (nonpathogenic hos t i n fec t ion ) .

(1) t h e rhizosphere sensu s t r i c to (= ou te r rhizosppere)

Table III Influence of Surface Sterilization of Rice Roots

Upon the Survival of Diazotrophic and Sulfate-Reducing Bacteriaa

Number of Bacteria Expressed on a Root Weight Basis

Percentage of 1-cm Long Root Segments Harboring Diazotrophs or Sulfate-Reducing Bacteria

Roots Washedb Roots Surface-Sterilizedc Roots Washedb Roots Surface-Sterilizedc with Sterile Water by Chloramine T with Sterile Water by Chloramine T

175 x lo6 100 100

O 67 O

3 m agawon and Diem, 1976, personal communication. bRhizoplane + endorhizosphere bacteria ‘Endorhizosphere bacteria

460 The TerrastriaZ Env$ronment

N 2 f i x a t i o n (C2H2) w a s s i g n i f i c a n t l y higher i n s tubb le than i n t h e con t ro l s o i l .

d e n i t r i f y i n g b a c t e r i a and a l s o active sulfate-reducing o r o the r anaerobic bac te r i a . act as energy sources f o r microorganisms, anaerobic hetero- t rophs con t r ibu te a c t i v e l y t o anaerobic t ransformations of t h e s o i l .

Beside diazotrophs, r ice debr i s may harbor active

A s long as such microenvironments

THE CONCEPT OF ULTRAMICROENVIRONMENT

Whereas microenvironments are r e l a t e d t o a volume commensurate i n s i z e wi th a given organism, ultramicroenviron- ments are charac te r ized by grada t ions i n ions o r molecules induced e i t h e r by organic o r inorganic s o l i d p a r t i c l e s (e.g., c lays , humic compounds) o r by o the r l i v i n g organisms. Ultramicroenvironments induced by s o l i d s , which have a l r eady been descr ibed by McLaren and S.kujins (1968) and H a t t o r i and H a t t o r i (1976) as molecular environments, are not d e a l t with here.

The concept of ultramicroenvironment induced by o the r organisms has no t y e t emerged c l ea r ly . i l l u s t r a t e t h i s concept. t he a s soc ia t ion occurr ing between Rhodopseudomonas capsuZatys and Azotobacter vineZandii (Figure 5). I n s p i t e of being an anaerobic bac te r i a , R. capsuzutus can grow w e l l when a s soc ia t ed

Two examples w i l l The f i r s t example is r e l a t e d t o

AZ. vinelandii

R. capsulatus

Slime substance

Figure 5. Schematic r ep resen ta t ion of a mixed c u l t u r e of Rhodopseudomonas capsuzutus and Azotobacter vineZandii (Okuda e t a l . , 1961).

with A. vinezandii even i n ae rob ic environments, t h e i n t e r - a c t i o n between R. capsuzutus and A. vinezandii occurr ing near o r on t h e i r cell membrane. The second example i s t h a t of

Paddg Soils, Peat, Coal 461

MethanobaciZZus omel imsk i i , which transforms e thånol and CO2 i n t o acetate and methane. Actual ly M. omelianskii is a mixed c u l t u r e of two microorganisms - a methane-producing b a c t e r i a (H) and another organism (S) t h a t oxides e thanol i n t o acetate and H2. are:

The r eac t ions operated by each organisms

Organism H: 4 H, + CO,-* CH, + 2 H,O

2 CH3CH20H + 2 H20-2 CH3-COOH + 4 H2 2 CH3CH20H + CO2 - 2 CH3-COOH + CH4 Organism S:

Organisms S does not grow proper ly on ethanol . But,

The i n t e r a c t i o n between i f both organisms are grown i n mixed cu l tu re , they grow p e r f e c t l y w e l l on e thanol and C02. t he organisms consis ts ' of an i n t e r s p e c i f i c t r a n s f e r of H2 (Bryant e t ai?, , 1967; Le Gal l , . 1977, personal communication). I n such a system, organism H induced an environment promoting t h e oxydation of e thanol i n t o acetate by organism S .

Of course the concept of ultramicroenvironment is not l imi t ed t o paddy f i e l d s and can be ex t rapola ted t o o ther s o i l types.

VARIATIONS OF MICROBIAL ACTIVITY I N MICROENVIRONMENTS

Such v a r i a t i o n s were c l e a r l y demonstrated i n t h e case of N2 f i x a t i o n i n t h e r ice rhizosphere. Since diazotrophs th r iv ing i n t h e rhizosphere depend upon the supply of energy by t h e p l a n t and s i n c e t h i s supply depends i t s e l f upon t h e p l a n t photosynthesis and t r ans loca t ion of energy y i e ld ing compounds towards , the r o o t s , one can p red ic t t h a t N2 f i x a t i o n by diazotrophs assoc ia ted t o t h e r o o t w i l l depend upon t h e f a c t o r s governingtkie p l an t physiology, e spec ia l ly l i g h t in- t e n s i t y and temperature. showed t h a t N2 f i x a t i d n f luc tua ted d iu rna l ly , with a midday peak a m i n i " l e v e l during t h e n igh t (Figure 6). Seasonal v a r i a t i o n s have been s t r e s s e d already i n t h i s chapter , e . g . , v a r i a t i o n s of N2 f i x a t i o n by blue-green a lgae induced by modi f ica t ion of l i g h t i n t e n s i t y reaching the f lood water layer .

Actual ly , in situ measurements

DIFFUSION OF METABOLIC PRODUCTS ORIGINATING FROM THE THE DIFFERENT MICROENVIRONMENTS

Since each of t h e microenvironments making up t h e paddy s o i l are t h e sites of d i f f e r e n t microbia l r eac t ions occurr ing most o f t en simultaneously, d i f f e r e n t metabol ic products accumulate a t the same t i m e , c r ea t ing g rad ien t s of concen- t r a t i o n around t h e most active sites. Thus t h e concent ra t ion of NJ&+-N i n the aerobic l a y e r tends t o decrease r ap id ly s ince NH4+-N is oxidized t o NO3'-N by n i t r i f y i n g b a c t e r i a ,

4 62

(u E O O

o

?

r

c \ d (u o w œ O - E e E o .-

The Terrestrial Environment

3c

20

10

O O

NIGHT DAY NIGHT

T

12 24 Hours of day

Figure 6. Diurnal v a r i a t i o n s of rhizosphere n i t rogen f i x a t i o n i n a r ice f i e l d assayed by ace ty lene reduct ion; ca l cu la t ed curve observed means and s tandard e r r o r s (shown by l i m i t s ) (Balandreau e t aZ., 1974).

Paddy SoiZs, Peat, Coa2 463

P which f i n d favorable environmental condi t ions i n t h i s l aye r . NHb+-N, r e s u l t i n g from ammonification of r o o t d e b r i s i n t h e anaerobic layer , d i f f u s e upwards i n t o t h e aerobic l aye r . This d i f f u s i o n process i s inf luenced by several f a c t o r s such as organic matter s t a t u s of t h e s o i l , c a t i o n exchange capac i ty , bulk dens i ty , and presence of reduced Fe and Mn (Ready e t al., 1976). t he anaerobic l aye r and i s subsequently d e n i t r i f i e d . Losses of Np and N20 through these simultaneous processes are re- ported t o be l a r g e (Broadbent and Tusneem, 1971; Yoshida and Padre, 1974). Thus, phys ica l d i f fus ion processes may enhance s p e c i f i c b i o l o g i c a l r eac t ions , which may be de t r imenta l t o t h e f e r t i l i t y s t a t u s o f t h e s o i l , such as d e n i t r i f i c a t i o n .

Simultaneously NO3--N r e a d i l y d i f f u s e s back down i n t o

REFERENCES

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ENVIRONMENTAL BIOGEOCHEMISTRY AND GEOMICROBIOL0GY Volume 2: The Terrestrial Environment

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