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A quantitative analysis of the variability in the activity of nitrifying organisms in a soil under pasture : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University

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A thes is presented in partial ful f i lment of the requirement s for

the degree of Doctor of Phi losophy at Massey University

Robert G.V. Bramley

1 9 89

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i ABSTRACT

vari ab i l i t y in the inputs , outputs and trans formations of mineral N under f ield condit ions makes the predict ive mode l l ing of the leaching of soil nitrate very d i f f icult . In an attempt to understand and quant i f y this variabi l i t y , the activity of nitr i fying organi sms in the Tokomaru s i l t loam ( a Typic f ragiaqua l f ) under pas ture was measured us ing a short-term nitr i f ication assay ( SNA ) . Spatial dependence of the variab i l i ty in SNA was examined using geos tatistical methods , and the e f fect on SNA of soil pH change through l iming , and of seasonal changes in soil temperature and moi s ture were inves t igated .

Nitr i f ier act ivity and associated soi l properties such as the amount of exchangeable ammonium and the soi l ni trate concentrat ion , were found to decrease in value w i th depth between 0 - 2 4 cm . The greatest decrease in SNA was observed between 0 - 9 cm depth , but due to the need for suf f icient quanti ties of soi l to make SNA measurements , and the des ire to avoid the poss ibi l ity of inhibitory ef fects of grass roots on nitr i f ication , soil was s ampled from the 3 -9 cm depth range for the bul k of the work reported here . Results i ndicated that the technique of sieving and mi xing samples was s at is factory f or removing de pth-dependen ce from the r esults for spa t i a l vari ab i l i ty and other analyses .

The spa t ial variab i l i ty of SNA , soi l No3 - , soi l mois ture content and the pH of the SNA incubation , which was assumed to approximate the f i eld soil pH , was invest igated over areas of 9 m2 and 6 2 5 m2 us ing a regular 1 1 x

1 1 square grid sampl ing des ign with minimum sample separat i ons of 30 cm and 2 . 5 m respect ively . However , the results of these analyses proved inconclusive , apparent ly due to the lack of samples separated. by lags that were suf f iciently short in relat ion to the overal l dimens ions of the sampl ing area . Accordingly , spa t i a l ana lysis of the above proper ties , together w i th exchangeable ammonium , was carried out over 6 2 5 m2 using a n es ted sampl ing design that permitted an adequate number of observation p a i n t s a t l a gs r anging f rom 1 2 . 5 c m t o 2 5 m . Thi s d e s i gn was a cons iderable improvement on the regular square des i gn , al though i t had a number of shor tcomings , not ably bias caus ed in the estimat ion of the samp l e vari ance d ue to t he nes ting o f a large number of data points

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w i thin a sma l l area , and bias caused in the estimat ion o f va lues of the s e m i va r i ance a t s ome l a gs- due to m i s s i ng samp l i n g points at some pos i t i ons in the sampl ing grid .

The v a l ues o f S N A , N0 3 - and ex chan geab l e ammonium were a l l highly variable and conformed to lognormal distribut ions . The range of spatial dependence in the variabi l i t y of SNA , soil N03 - and incubation pH was 2 . 4 , 5 . 4 and 6 . 1 m respect ive ly . Exchangeabl e ammonium , SNA , soil No3 - and incubation pH varied i sotropi cally w ithin the sampl ing area but Ex­

NH4• showed no spatial dependenc e . Soi l moisture content was s trongly anisotropic , and showed no spa t ial dependence in one d irection , but clear evidence o f dr i f t in a p er pend i cular d i r ec t i on . These results are d i s c u s s e d in r e l a t i o n t o t he mos t e f f i c i ent s ampl ing s trategy for est imation of the mean field N03 - concentration . I t was concluded that suf f ic i ent sma l l loca l i zed c lusters of samples should be taken to give a low s tandard error of the mean , w i th each cluster separated by at l east 5 m . I n the case of the Tokomaru s i l t loam , 20 clus ters , each compris ing 5 samples ( bulked ) , would be required for estimation of the mean f ield n itrate concentrat i on with 9 5 % probability of

0

being wi thin ± 5% of �' the true mean . This represents a l arge sampl ing ef fort .

The a c t i v i t y o f n i t r i f i e r s w a s s tud ied in relat ion to soil pH and seasona l changes in soil mois ture and temperature over two consecut ive years i n an attempt to explain the spatial variabi l i ty in SNA values . The pH opti mum for nitrif ier activity ( pHopt ) was def ined for four var iates of the Tokomaru s i l t loam w i t h d i f ferent l i ming hi s torie s . Values of pHopt which varied between the four soi ls in the range 5 . 9 2 - 6 . 4 5 did not v a r y m a r ke d l y w i th s ea s on , and i t was found that the form of the rel a t i onship bet ween SNA and pH remained c ons tant wi th t ime . I t was further observed that the add i t ion of l ime in 1 9 87 had the ef fect of rais ing the mean soil pH and pHopt in previously-unl imed soi l , but had

negligible e f fect on ei ther the soi l pH or pHopt in soi l that had been l imed in 1 9 8 2 . The significance of heterotrophic relat ive to autotrophic n i t r i f icat ion could not be discerned .

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iii

No sign i f icant relationships could be found for the four soils between soil pH , pHopt, SNA, soil moisture content and soi l temperature at 3 0 cm dept h . Va lues of SNA ( pmol N g -1 so i l h- 1 ) at pHopt ( SNAopt) wer e calcul a t ed fr om equa tions f i t ted t o p l o t s of SNA vs . the pH of SNA

incuba t ion , a nd thes e show a more obvious seasona l trend . SNA va lues calculated for the prevail ing so i l pH (SNApH) were never very d i f ferent from v alues of SNAopt and follow a 1 : 1 rela t i onship over a range of values f rom 0 . 0 1 5 - 0 . 1 1 0 pmol g-1 h-1 ; that i s , the nitr i f ier activity in the s o i l , i r r e spe c t i ve o f va r i a t i o n s t ha t were ra ndo m ( unknown i n f l uences ) or a s s oc i a ted w i th s e a s o n a l var iables ( temperature and moi sture ) , was near the opt imum with respect to the soi l pH a t the time of samp l ing .

The e f f ect of soil moisture variat ion on n i trif ier act ivity was further invest i gated in an experiment in which soil samples were s tored for 1 2 4 days a t d i f ferent soi l mois ture tens ions . The opt imum moisture conditions for n i t r i f ier activity in the Tokomaru s i l t loam prevai led at pF 3 . 3 9 . However , thi s optimum was less clearly def ined than was the pHopt • S ince the s o i l moisture status changes cons iderably with season, whi ls t soi l pH does not , it was concluded that nitrif iers were more tolerant of changes

in pF than changes in pH .

Compa r i son of these with published results indicates that not only is the soi l n i trif ier popul ation dynamic , and changes in response to changes in i t s environmen t , but the degree to which n i trif ier activi t y i s a f fected by var ious soi l properties is soi l - spec i f ic . It is therefore concluded that the spatial variabi l i ty of nitrif ier activi ty will a l so be so i l ­ speci f ic , and that dif ferent soils are l ikely t o have dif ferent ranges o f spa t i a l dependence for the parameters of mineral N. Furthermorer the f act that SNA i s not the only factor governing the soi l No3- concentration , and t h a t o t h e r f ac tors s uch as p l a n t uptake and leaching are a l so impo r t an t , indicates that SNA var i ab i l i t y i s not necessar i ly a good e s t i m a t o r of s o i l N03- var i abi l i t y . Th i s conc l us i o n i s c e r t a inly suppor ted by the geostatist ical aspects of this work .

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ACKNOWLEDGEMENTS

I would like to thank the fol lowing people for their part in seeing this proj ect through to complet ion :

P r o f e s s o r R . E . Wh i t e f o r h i s s u p e rv i s i o n a nd gui dance throughout . The support given in l oco paren ti s by Bob and his w i fe , Annet t e , on arrival in this s trange ( ! ) country and their friendship thereaf ter has been very greatly appreciated .

D r A . N . Macgregor for hi s supervis ion .

Drs D . R . Scotter , P . R . Darrah , A . B . McBratney and A . Swi f t , and Messrs L . D . Currie, M . Eggel s , Mrs H . Murphy and Mrs A . Rouse for their assistance at various s tages of the proj ect .

The s t a f f and po s t graduate s tude n t s of t he S o i l S c ience Department for providing the re laxed and friendly a tmosphere which made l i fe at Massey so enj oyable .

The Vice-Chancel lor of Massey Univers ity , Dr T . N . M . Waters , for making the necessary funds avai lable for this work .

Fina l l y I would l ike to thank my parents , John and Rosal ind Bramley , for providi ng a l l that made starting this work possible , and Jo T o mp k i n s , who s e suppor t a nd a f f e c t i o n w a s t h e much n e eded inspirat ion for its complet ion.

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V

A QUANTITATIVE ANALYSIS OF THE VARIABILITY IN

THE ACTIVITY OF NITRIFYING ORGANISMS IN A SOIL UNDER PASTURE

TABLE OF CONTENTS

Abstract . . . . . . . . . . . . . . . . . .. . . . . . . . .. . . . . . . . . .. . . . . . . . .. .. . . . . . . . . . . . . . . .i

Acknow ledgments . . . . . . .. . . . .. . . . . . . .. . . . . . . . . . .. . . . . . . .. . . . . . . . . . . . . . . . .iv

Table of contents .. . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . .. . . . . . . . . . . . . . . .v

List o f Figures . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . .. . . . . . . . .. . . . . . . . .. . . . . . .xi

List o f Tables . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . .. . . . . .. . . . . . . . . . . . . . . .xvi

SECTI ON I . INTRODUCTION CHAPTER 1. INTRODUCTION AND AIMS OF THE PROJECT . . . . . . . . . . . . . . . .1

i . Background to the proj ect - the nitrate leaching problem . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . .1

i i . Nitrate leaching models . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3

i i i . The aim of the proj ect . . . . . . .. . . . . . . . . . . . . . . . . . . . . . .5

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CHAPTER 2 . NITRIFICATION IN SOILS: A REVIEW . . . . . . . 7

i . The factors a f fect ing ni tri f icat ion and

mineral i zation . . .. . . .. . . . . . . . . . . . . . . . . . . . . . . . . . .9 i i . Mode l l ing of nitrif ication . . . . . . . . . . . . . . . . . . . . . . . . . 1 7 i i i . A comment on measured nitrif ication rates . . . . . .. . . . 2 3 iv . Conc lus ion . . . .. . . . . . . . . . . . .. . . . . . .. . . . . 2 4

CHAPTER 3 . A THEORETICAL CONSIDERATION OF SPATIALLY

DEPENDENT VARIABILITY . . . . . . . . -. . . 2 5

i . Why do we need geostatistics ? . . . . . . . . . . . . . . . 2 5

i i . Some pre l i minary data analysis using class ical

statist ics . . . .. . . . .. . . . . . . . . . . . . . . . ... . . . . . . . . . . . . 28 i i i . Stationari ty and the semi -variance . . .. . .. · . . . . . . . . . . 3 2 i v . The var iogram . .. . . . . . .. . . . . . . . . . . .. . . . . . . . . . . . . . . 3 5 v . Spatial variation in two dimens i ons .. . . . . . . . . . . .. . . 40 vi . Other variogram models . . . . . . . . . . . . . . . .. . . . . . . . . . . 4 7 v i i . Conclus ions . . .. . . . . . . . . . . . .. . . . .. . . . . . .. . . . . . . 5 1

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vi i CHAPTER 4. EXPERIMENTAL METHODOLOGY . . . . . . . . .. . . . . . . . . . . . . . . . . . 5 2

A . THE SHORT-TERM NITRIFICATION ASSAY . . . .. . . . . . . . . . . . . . . . 5 2

i . Select ion of incubation media for SNA

analyses . . . 5 3

i i . Linearity of nitr i f ication rate in the

Tokomaru s i l t loam . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . .5 4

i i i . Select ion o f ammonium subs trate concentration

for SNA analyses . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . .5 8 iv . Ana lysis of exchangeable ammonium . .. . . . . . . . .. . . . . . .6 1

B . FIELD SAMPLING . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . .6 2 i . S i te detai l s . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . 6 2 i i . Soil sampl ing . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . .6 3

i i i . Correlation between moisture contents o f

s i eved and uns ieved soil . . . . . . . . . . . . .. . . . . . . . . . . . . . 6 3

C . STORAGE OF SAMPLES PRIOR TO SNA MEASUREMENTS . . . . : . . . 6 7

i . Ef fects of drying and s torage on mineral

nitrogen . . .. . . . . . .. . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . .67 i i . Ef fects of drying and storage on soil biomass . . . . . .69

D . CONCLUS IONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . ... . . . . . . . . . . .7 6

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SECTION I I . AN ANALYSIS OF SPATIAL VARIABILITY IN NITRIFIER 'ACTIVITY

CHAPTER 5 . VARIABILITY IN NITRIFIER ACTIVITY WITH DEPTH

AND DISTANCE . . . . .. . .. . . . . . . . .. . . . . . . . . . . . . . . . . . . . . .7 8

A . DEPTH DEPENDENT VARIABI LITY . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .7 8 i . Methods and Materials . . . . . . . . . . . . . .. .. . . . . . . . . . . . . .7 9 i i . Results . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8 1 i i i . D i scus s ion . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9 3

B . SPATIALLY DEPENDENT VARIABILITY . . . . . , . . . , . . . 9 6 i . Methods and Materials . . . . . . . . . . . . . . . . . . . . . . .. . . . . . .9 7 i i . Results . . . . . . . . . . . . . .. . . . . . . . . . .. . . . . .. . . . . . . . . . . . . .9 8 i i i . Discuss ion . . . . . .. . . . . .. . . . . . . . . . . . . . . . . .. . . . . . . . . .1 0 8

CHAPTER 6 . SPATIAL VARIABILITY OF NITRIFIER ACTIVITY -

A MORE REFINED ANALYSIS . . . . . . , . . . 1 1 6

i . Methods and Materi als . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 2 1 i i . Resul t s . . . . . . . . . . . . .. . . .. . . . . . . . . . . . . . . . . . . . . . . . . .1 2 1 i i i . Di scuss ion . . . . . . . . . . . .. . . . . . . . . . . . . . .. . . . . . . . . . . . . 1 2 5 iv . Conc lus ions and recommendations for future

samp ling s trategy .. . . . . .. . . . . . . . . . . . . . . . . . . . . . . .. .1 4 0

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SECTION I I I . FACTORS AFFECTING NITRIFIER ACTIVITY

ix

CHAPTER 7 . THE EFFECT OF pH , MOISTURE AND TEMPERATURE ON

NITRIFIER ACTIVITY . . . . . . . . 1 4 4

i . Methods and Materials . . . . . . . . . . . . . . .. . . . . . . . . . . . . . 1 4 4 i i . Results . . . . .. . . . . . .. . . ; . . . ; . . . . ·. ; . . . 1 4 9 i i i . Di scussion . . . . . . . . . . .. . . . .. . . . . . . . . . . . . . . . . .. . . .. . 1 68 iv . Conclusions . . . . . .. .. .. . . . . . . . . . . .. . . . . . . . . . . . . . . 1 7 6

CHAPTER 8 . A FURTHER INVESTIGATION OF THE EFFECT OF

MOISTURE ON NITRIFIER ACTIVITY . . .. . . . . . . . . . . . . . . . . 1 7 7

i . Methods and Materials . . . 1 7 8 i i . Results . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 8 0 i i i . Di scussion . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . .1 9 3

CHAPTER 9 . HETEROTROPHIC NITRIFICATION - EXACTLY WHAT

HAS BEEN MEASURED BY THE SNA ? . .. . . . . . . . . . . . . . . . . . 1 9 8

i . Methods and Materials . . . . . . . . . . . . .. . . . . . . . , . . . 2 0 1 i i . Results . .. . . . . . . . . . . . . . . . . .. . . . . .. . . . . .. . . . . . . . . . .2 0 3 i i i . D iscuss ion . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . .2 0 9 iv . Conclus ion .. . . . . . . . .. . . . ... . . . . . . . . . . . . . . . . . . . . . . . . 2 1 2

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SECTION IV .

CHAPTER 10. GENERAL DISCUSSION, CONCLUSI ONS AND

RECOMMENDATIONS FOR FURTHER WORK .. . . . . . . . ., . . . 2 1 3

A . A CRITIQUE OF THE GEOSTATI STICAL TECHNIQUES USED FOR THE ASSESSMENT OF SPATI AL VARIABILITY IN

NITRIFIER ACTIVITY . . . . . . . .. . . . . . . .. . . . . . . . . . . . . . . . . . . . . .2 1 3 i . Problems caused by ani sotropy . .. . . . . . .. . . . . . . . . . . .2 1 4

i i . Problems caused by changes in the sample variance and variation in the variogram model

w i th time and the scale o f sampl ing . . . 2 1 8

i i i . The relationship between the s i l l and the

sample variance . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2 2 5 iv . Cros svariogram ana lys i s . . . : . . . 2 3 0

B . SOME CONCLUDING COMMENTS ON VARIABILITY IN

NITRIFIER ACTIVITY . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .2 3 2

REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . .. . . . . . . . . .. . . . . .2 3 5 APPENDIX I . COMPUTER PROGRAMS . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 5 2 GAMMAH . . . . . . . . . . . . . .. . . . . . . . . . . . .. . . . . . . . . . . . . . . . . 2 5 3 COVGM . . . 2 5 8

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Figure 3 . 1 Figur e 3 . 2

F igur e 3 . 3

Figure 3 . 4

Figure 3 . 5

Figure 3 . 6

Figure 3 . 7

Figure 3 . 8

Figure 3 . 9

F igure 3 . 1 0

x i

LIST O F F IGURES

Distribut ion o f a set of 2 5 pH data . . . .. . . . . . . . . 2 9

Change in the mean and variance w i th increas ing

sample number for a set of 25 pH data . . . . . . . . . 3 1

Experimenta l variogram for the 2 5 pH. data , and the number of pairs of points s eparated by each

lag . .. . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . 3 6

Change in the value of ¥ ( h ) as the number o f pairs A

of data points used to calculate it increases . . . . . . 3 8

Experimental variogram for soi l pH with linear models f i t ted by ordinary and least squares

optimi zat ion . . . . . . . . . . . . . . . . . . . . . . . . . . .. 3 9

1 2 1 equally spaced pH data sampled f rom a regular

1 1 x 1 1 square grid . . . . .. . . . . . . . . . . . .. . . . 4 1

Distribution of the 1 2 1 pH data shown in Figure

3 . 6 . . . 4 2

Change i n the mean and variance with increas ing

sample number for the set of 1 2 1 pH data . . . . . . . . . 4 4

Change i n the number o f pairs o f points separated by each lag as the length of the grid s ide

increases from 1 to 1 0 lag uni ts . . . . . .. . . . . . . . . . . . . . . 4 5

Devel opment o f an experimental vari ogram a s the number of samples used to est imate it increases as the length of the grid side increases from 2

( 4 samples ) to 1 0 lag units ( 1 2 1 samples ) . . . .. . . . . . 4 6

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Figure 3 . 1 1

F igure 4 . 1

Figure 4 . 2

Figure 4 . 3

Figure 4 . 4

Figure 4 . 5

Figure 5 . 1

F i gure 5 . 2

Figure 5 . 3

Experimental var iogram for the 1 2 1 pH data f i tt ed with a spher ica l model by weighted least squares

opt imization . . . 5 0

L inearity o f ni trificat ion rate over 1 9 hours i n

the Tokomaru s i l t loam a t 2 2 oc . . . . . . . . 5 6

Mean monthly weather data ( 1 92 8 - 1 98 0 ) for the D . S . I . R Grasslands weather stat ion , Palmers ton

North ( N . Z . Meteorologica l service , 1 98 3 ) . . . 6 4

Corre lation between the gravimetric moisture contents of s ieved ( < 2mm ) and unsieved Tokomaru

s i l t loam . . . 6 6

p H optima curves for nitri f i er activity in fresh

soil and soil that had been s tored for 3 weeks . . . 7 4

Common pH opt imum curve f i tted t o SNA data for

fresh and stored soil . . . 7 5

Change i n bul k dens ity and mean volumetri c moisture content with depth in the Tokomaru s i l t loam

sampled in mid May . . . 8 2

Depth pro f i les of ( a ) SNA , ( b ) No3 - , ( c ) Ex-NH4 · , ( d ) incubation pH , ( e ) total carbon , ( f ) total nitrogen , ( g ) C/N ratio , ( h ) tota l phosphorus , and ( i ) % mineral N in the Tokomaru �i l t loam.

sampled in mid May . . . 8 4

Distribution with depth of total carbon , ni trogen , phosphorus , C/N ratio and SNA expressed as a % of

thei r maximum values . . . ... . . 92

Referensi

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