Soil Research Soil Research Society
Soil, land care and environmental research
RESEARCH ARTICLE

Seasonal changes in microbial function and diversity associated with stubble retention versus burning

F. C. Hoyle A B and D. V. Murphy A

A School of Earth and Geographical Science, Faculty of Natural and Agricultural Sciences, University of Western Australia, Crawley, WA 6009, Australia.

B Corresponding author. Email: fhoyle@agric.wa.gov.au

Australian Journal of Soil Research 44(4) 407-423 http://dx.doi.org/10.1071/SR05183
Submitted: 21 November 2005  Accepted: 21 February 2006   Published: 27 June 2006

Abstract

The long-term (16-year) effect of stubble management (i.e. retained or burnt) on the size of the microbial community (microbial biomass-C and -N), microbial community structure (PLFA), and function (CO2-C evolution, gross N transformation rates, enzymatic activity, and community level physiological profiles) was investigated on 4 occasions during a single wheat-growing season using soil collected from the low-rainfall (<250 mm) region of Western Australia. Significant differences (P < 0.001) in microbial community structure and function were determined for different sampling times by phospholipid fatty acid (PLFA) analyses and community level physiological profiles (CLPP). However, neither PLFA nor CLPP analyses identified differences between stubble treatments. In contrast to total soil organic matter-C, for which no treatment differences were evident, microbial biomass-C was 34% and CO2-C evolution 61% greater in stubble-retained treatments than in burnt-stubble treatments in the 0–0.05 m soil layer. Seasonal increases in microbial biomass-C (P < 0.001) were on average twice as large and CO2-C evolution (P < 0.001) nearly 4 times greater in September during crop flowering compared with other sampling times. In contrast, microbial biomass-N remained constant throughout the entire sampling period. Stubble-retained treatments also demonstrated significantly greater (P < 0.05) levels of arginine ammonification, acid phosphatase and β-glucosidase enzyme activity on average compared with burnt-stubble treatments. However, the effect (P = 0.05) of stubble treatment on gross N mineralisation, nitrification, or immobilisation rates was seasonally dependent with burnt-stubble treatments demonstrating lower gross N mineralisation rates than retained-stubble treatments in November. Gross N mineralisation was lower (37–83% on average) than potential gross nitrification rates (estimated in the presence of excess NH4+) measured from May to September. The rate of potential gross nitrification was observed to decline significantly (P = 0.06) in November and as a result, more closely matched gross N mineralisation rates. Potential gross nitrification rates were also up to 6 times greater than microbial immobilisation of NH4+, indicating that this would be the primary consumptive process in the presence of NH4+. Whilst potential nitrification rates in the presence of excess NH4+ were high, low soil NO3 concentrations indicate that plant/microbial demand for NO3 and NH4+ exceeded the supply capacity. For example, actual gross nitrification rates (determined in the presence of 15N-labelled NO3-) were only greater than gross N mineralisation in May, indicating N supply constrained nitrification at other sampling times. Findings illustrate that increased wheat yields of 31% in this study were associated with the retention of stubble. Further they demonstrate that changes in stubble management significantly influenced the mass and activity of microorganisms (and in some cases N cycling), whilst having little influence on community diversity.

Additional keywords: 15N isotopic pool dilution, FLUAZ, nitrogen, carbon.


References

Alef K , Nannipieri P (Eds) (1995) ‘Methods in applied soil microbiology and biochemistry.’ (Academic Press: London)

Amato M Ladd JN Ellington A Ford G Mahoney JE Taylor AC Walsgott D 1987 Decomposition of plant material in Australian soils. IV. Decomposition in situ of 14C and 15N-labelled legume and wheat materials in a range of southern Australian soils. Australian Journal of Soil Research 25 95 105 doi:10.1071/SR9870095

Anderson MJ 2001 A new method for non-parametric multivariate analysis of variance. Ecology 26 32 46

Anderson MJ Robinson J 2003 Generalised discriminant analysis based on distances. Australian & New Zealand Journal of Statistics 45 301 318
doi:10.1111/1467-842X.00285

Anderson MJ Willis TJ 2003 Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84 511 525

Anderson T-H Domsch KH 1985 Determination of ecophysiological maintenance carbon requirements of soil microorganisms in a dormant state. Biology and Fertility of Soils 1 81 89
doi:10.1007/BF00255134

Andersson M Michelsen A Jensen M Kjøllera A 2004 Tropical savannah woodland: effects of experimental fire on soil microorganisms and soil emissions of carbon dioxide. Soil Biology and Biochemistry 36 849 858 doi:10.1016/j.soilbio.2004.01.015

Andrén O Paustian K 1987 Barley straw decomposition in the field: a comparison of models. Ecology 68 1190 1200

Angus JF 2001 Nitrogen supply and demand in Australian agriculture. Australian Journal of Experimental Agriculture 41 277 288
doi:10.1071/EA00141

Atwell BJ Fillery IRP McInnes KJ Smucker AJM 2002 The fate of carbon and fertiliser nitrogen when dryland wheat is grown in monoliths of duplex soil. Plant and Soil 241 259 269 doi:10.1023/A:1016141800033

Bandick AK Dick RP 1999 Field management effects on soil enzyme activities. Soil Biology and Biochemistry 31 1471 1479 doi:10.1016/S0038-0717(99)00051-6

Barz W 1970 Isolation of rhizosphere bacterium capable of degrading flavonoids. Phytochemistry 9 1745 1749 doi:10.1016/S0031-9422(00)85586-7

Bending GD Putland C Rayns F 2000 Changes in microbial community metabolism and labile organic matter fractions as early indicators of the impact of management on soil biological quality. Biology and Fertility of Soils 31 78 84 doi:10.1007/s003740050627

Bending GD Turner MK Jones JE 2002 Interactions between crop residue and soil organic matter quality and the functional diversity of soil microbial communities. Soil Biology and Biochemistry 34 1073 1082 doi:10.1016/S0038-0717(02)00040-8

Bonde TA Nielsen TH Miller M Sorensen J 2001 Arginine ammonification assay as a rapid index of gross N mineralization in agricultural soils. Biology and Fertility of Soils 34 179 184 doi:10.1007/s003740100395

Caravaca F Masciandaro G Ceccanti B 2002 Land use in relation to soil chemical and biochemical properties in a semiarid Mediterranean environment. Soil & Tillage Research 68 23 30 doi:10.1016/S0167-1987(02)00080-6

Carter MR Mele PM 1992 Changes in microbial biomass and structural stability at the surface of a Duplex soil under direct drilling and stubble retention in north-eastern Victoria. Australian Journal of Soil Research 30 493 503 doi:10.1071/SR9920493

Chan KY Roberts WP Heenan DP 1992 Organic carbon and associated soil properties of a Red Earth after 10 years of rotation under different stubble and tillage practices. Australian Journal of Soil Research 30 71 83 doi:10.1071/SR9920071

Choromanska U DeLuca TH 2001 Prescribed fire alters the effect of wildfire on soil biochemical properties in a ponderosa pine forest. Soil Science Society of America Journal 65 232 238

Cookson WR Abaye DA Marschner P Murphy DV Stockdale EA Goulding KWT 2005 The contribution of soil organic matter fractions to carbon and nitrogen mineralization and microbial community size and structure. Soil Biology and Biochemistry 37 1726 1737
doi:10.1016/j.soilbio.2005.02.007

Cookson WR Beare MH Wilson PE 1998 Effects of prior crop residue management on microbial properties and crop residue decomposition. Applied Soil Ecology 7 179 188 doi:10.1016/S0929-1393(97)00032-2

Cookson WR Murphy DV 2004 Quantifying the contribution of dissolved organic matter to soil nitrogen cycling using 15N isotopic pool dilution. Soil Biology and Biochemistry 36 2097 2100 doi:10.1016/j.soilbio.2004.05.013

Dalias P Anderson JM Bottner P Coûteaux M-M 2001 Long-term effects of temperature on carbon mineralization processes. Soil Biology and Biochemistry 33 1049 1057 doi:10.1016/S0038-0717(01)00009-8

Davidson EA Belk E Boone RD 1998 Soil water content and temperature as independent or confounded factors controlling soil respiration in a temperate mixed hardwood forest. Global Change Biology 4 217 227 doi:10.1046/j.1365-2486.1998.00128.x

De-Bano L Conrad C 1978 The effect of fire on nutrients in a Chaparral ecosystem. Ecology 59 489 497

Degens BP 1998 Microbial functional diversity can be influenced by the composition of simple organic substrates added to soil. Soil Biology and Biochemistry 30 1981 1988
doi:10.1016/S0038-0717(98)00070-4

Degens BP Harris JA 1997 Development of a physiological approach to measuring the catabolic diversity of soil microbial communities. Soil Biology and Biochemistry 29 1309 1320 doi:10.1016/S0038-0717(97)00076-X

Degens BP Schipper LA Sparling GP Duncan LC 2000 Decreases in organic C reserves in soils can reduce the catabolic diversity of soil microbial communities. Soil Biology and Biochemistry 32 189 196 doi:10.1016/S0038-0717(99)00141-8

Degens BP Schipper LA Sparling GP Duncan LC 2001 Is the microbial community in a soil with reduced catabolic diversity less resistant to stress or disturbance? Soil Biology and Biochemistry 33 1143 1153 doi:10.1016/S0038-0717(01)00018-9

Degens BP Vojvodic-Vukovic M 1999 A sampling strategy to assess the effects of land use on microbial functional diversity in soils. Australian Journal of Soil Research 37 593 601

Diaz-Ravina M Prieto A Baath E 1996 Bacterial activity in a forest soil after soil heating and organic amendments measured by the thymidine and leucine incorporations technique. Soil Biology and Biochemistry 28 419 426
doi:10.1016/0038-0717(95)00156-5

Dickens HE Anderson JM 1999 Manipulation of soil microbial community structure in bog and forest soils using chloroform fumigation. Soil Biology and Biochemistry 31 2049 2058 doi:10.1016/S0038-0717(99)00128-5

Eivazi F Tabatabai MA 1977 Phosphatases in soils. Soil Biology and Biochemistry 9 167 172 doi:10.1016/0038-0717(77)90070-0

Eivazi F Tabatabai MA 1988 Glucosidases and galactosidases in soils. Soil Biology and Biochemistry 20 601 606 doi:10.1016/0038-0717(88)90141-1

Fernandez I Cabaneiro A Carballas T 1997 Organic matter changes immediately after a wildfire in an Atlantic forest soil and comparison with laboratory soil heating. Soil Biology and Biochemistry 29 1 11 doi:10.1016/S0038-0717(96)00289-1

French RJ Schultz JE 1984 Water use efficiency of wheat in a Mediterranean-type environment. I. The relation between yield, water use and climate. Australian Journal of Agricultural Research 35 743 764 doi:10.1071/AR9840743

Gander LK Hendricks CW Doyle JD 1994 Interferences, limitations and an improvement in the extraction of cellulase activity in soil. Soil Biology and Biochemistry 26 65 73 doi:10.1016/0038-0717(94)90196-1

Gardner WK Barber DA Parbery DG 1983 The acquisition of phosphorus by Lupinus albus L. III. The probable mechanism by which phosphorus movement in the soil/root interface is enhanced. Plant and Soil 70 107 124 doi:10.1007/BF02374754

Georges T Dittert K 1998 Improved diffusion technique for N-15 : N-14 analysis of ammonium and nitrate from aqueous samples by stable isotope spectrometry. Communications in Soil Science and Plant Analysis 29 361 368

Grierson PF Adams MA 2000 Plant species affect acid phosphatase, ergosterol and microbial P in a Jarrah (Eucalyptus marginata Donn ex Sm.) forest in south-western Australia. Soil Biology and Biochemistry 32 1817 1827
doi:10.1016/S0038-0717(00)00155-3

Hatfield JL Sauer TJ Prueger JH 2001 Managing soils to achieve greater water use efficiency: a review. Agronomy Journal 93 271 280

Heenan DP Chan KY Knight PG 2004 Long-term impact of rotation, tillage and stubble management on the loss of soil organic carbon and nitrogen from a Chromic Luvisol. Soil & Tillage Research 76 59 68
doi:10.1016/j.still.2003.08.005

Herrmann A , Witter E , Kätterer T (2004) Can N mineralization be predicted from soil organic matter? Carbon and gross N mineralization rates as affected by long-term additions of different organic amendments. In ‘Controlling nitrogen flows and losses’. (Eds DJ Hatch, DR Chadwick, SC Jarvis, JA Roker) pp. 113–121. (Wageningen Academic Publishers: The Netherlands)

Hope CFA Burns RG 1987 Activity, origins and location of cellulases in a silt loam soil. Biology and Fertility of Soils 5 164 170 doi:10.1007/BF00257653

Hoyle FC Murphy DV Fillery IRP 2006 Temperature and stubble management influence microbial CO2-C evolution and gross N transformation rates. Soil Biology and Biochemistry 38 71 80 doi:10.1016/j.soilbio.2005.04.020

Joergensen RG Brookes PC Jenkinson DS 1990 Survival of the soil microbial biomass at elevated temperatures. Soil Biology and Biochemistry 22 1129 1136 doi:10.1016/0038-0717(90)90039-3

Kamphake LJ Hannah SA Cohen JM 1967 Automated analysis for nitrate by hydrazine reduction. Water Research 1 205 216 doi:10.1016/0043-1354(67)90011-5

Kempers AJ Luft AG 1988 Re-examination of the determination of environmental nitrate as nitrite by reduction with hydrazine. The Analyst 113 1117 1120 doi:10.1039/an9881301117

Killham K Sinclair AH Allison MF 1988 Effect of straw addition on composition and activity of soil microbial biomass. Proceedings of the Royal Society Edinburgh 94 135 143

Kirchner MJ Wollum AG King LD 1993 Soil microbial populations and activities in reduced chemical input agroecosystems. Soil Science Society of America Journal 57 1289 1295


Kirkham D Bartholomew WV 1954 Equations for following nutrient transformations in soil, utilizing tracer data. Soil Science Society of America Proceedings 18 33 34


Kirschbaum MUF 1995 The temperature dependence of soil organic matter decomposition, and the effect of global warming on soil organic C storage. Soil Biology and Biochemistry 27 753 760
doi:10.1016/0038-0717(94)00242-S

Kiss S Dragan-Bularda M Radulescu D 1975 Biological significance of enzymes in soil. Advances in Agronomy 27 25 91

Krom M 1980 Spectrophotometric determination of ammonia; a study of modified Berthelot reaction using salicylate and dichloroisocyanurate. The Analyst 105 305 316
doi:10.1039/an9800500305

Ladd JN (1978) Origin and range of enzymes in soil. In ‘Soil enzymes’. (Ed. RG Burns) pp. 51–96. (Academic Press: London)

Littleboy M Freebairn DM Hammer GL Silburn DM 1992 Impact of soil erosion on production in cropping systems. II. Simulation of production and erosion risks for a wheat cropping system. Australian Journal of Soil Research 30 775 788 doi:10.1071/SR9920775

Magurran AE (1988) ‘Ecological diversity and its measurement.’ (Croom Helm: London)

Marschner B Bredow A 2002 Temperature effects on release and ecologically relevant properties of dissolved organic carbon in sterilized and biologically active soil samples. Soil Biology and Biochemistry 34 459 466 doi:10.1016/S0038-0717(01)00203-6

Mary B Recous S Robin D 1998 A model for calculating nitrogen fluxes in soil using 15N tracing. Soil Biology and Biochemistry 30 1963 1979 doi:10.1016/S0038-0717(98)00068-6

Mayfield AH Clare BG 1984 Effects of common stubble treatments and sowing sequences on scald disease (Rhynchosporium secalis) in barley crops. Australian Journal of Agricultural Research 35 799 805 doi:10.1071/AR9840799

McArdle BH Anderson MJ 2001 Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82 290 297

McArthur WM (1991) ‘Reference soils of south-western Australia.’ (Eds DAW Johnston, LJ Snell) (Department of Agriculture: Perth, W. Aust.)

Murphy DV Fillery IRP Sparling GP 1998 Seasonal fluctuations in gross N mineralization, ammonium consumption, and microbial biomass in a Western Australian soil under different land uses. Australian Journal of Agricultural Research 49 523 535
doi:10.1071/A97096

Murray GM Heenan DP Taylor AC 1991 The effect of rainfall and crop management on take-all and eyespot of wheat in the field. Australian Journal of Experimental Agriculture 31 645 651 doi:10.1071/EA9910645

Neary DG Klopatck CC DeBano LF Folliott PF 1999 Fire effects on below ground sustainability: a review and synthesis. Forest Ecology and Management 122 51 71 doi:10.1016/S0378-1127(99)00032-8

Orr DM Paton CJ Lisle AT 1997 Using fire to manage species composition in Heteropogon contortus (black speargrass) pastures. 1. Burning regimes. Australian Journal of Agricultural Research 48 795 802 doi:10.1071/A96130

Powlson DS Brookes PC Christensen BT 1987 Measurement of microbial biomass provides an early indication of changes in total soil organic matter due to straw incorporation. Soil Biology and Biochemistry 19 159 164 doi:10.1016/0038-0717(87)90076-9

Raich JW Schlesinger WH 1992 The global carbon dioxide flux in soil respiration and its relationship to vegetation and climate. Tellus. Series B, Chemical and Physical Meteorology 44 81 99

Raison RJ 1979 Modification of the soil environment by vegetation fires, with particular reference to nitrogen transformations: a review. Plant and Soil 51 73 108
doi:10.1007/BF02205929

Rayment GE , Higginson FR (1992) ‘Australian laboratory handbook of soil and water chemical methods.’ (Inkata Press: Melbourne)

Recous S Aita C Mary B 1998 In situ changes in gross N transformations in bare soil after addition of straw. Soil Biology and Biochemistry 31 119 133 doi:10.1016/S0038-0717(98)00113-8

Reichstein M Bednorz F Broll G Kätterer T 2000 Temperature dependence of carbon mineralization: conclusions from a long-term incubation of subalpine soil samples. Soil Biology and Biochemistry 32 947 958 doi:10.1016/S0038-0717(00)00002-X

Ross DJ Scott NA Tate R Rodda NJ Townsend JA 2001 Root effects on soil carbon and nitrogen cycling in a Pinus radiata D. Don plantation on a coastal sand. Australian Journal of Soil Research 39 1027 1039 doi:10.1071/SR00058

Russell CA Fillery IRP 1996 Estimates of lupin below-ground biomass nitrogen, dry matter, and nitrogen turnover to wheat. Australian Journal of Agricultural Research 47 1047 1059 doi:10.1071/AR9961047

Smil V 1999 Crop residues: agriculture’s largest harvest. Bioscience 49 299 308

Spiro RG 1966 Analysis of sugars found in glycoproteins. Methods in Enzymology 8 7


Stockdale EA Hatch DJ Murphy DV Ledgard SF Watson CJ 2002 Verifying the nitrification to immobilisation ratio (N/I) as a key determinant of potential nitrate loss in grassland and arable soils. Agronomie 22 831 838
doi:10.1051/agro:2002060

Stynes BA Wise JL 1980 The distribution and importance of annual ryegrass toxicity in Western Australia and its occurrence in relation to cropping rotations and cultural practices. Australian Journal of Agricultural Research 31 557 569 doi:10.1071/AR9800557

Tabatabai MA (1994) Enzymes. In ‘Methods of soil analysis. Part 2. Microbiological and biochemical properties’. (Eds RW Weaver, S Augle, PJ Bottomly, Q Berdicek, Q Smith, A Tabatabai, A Wollum) pp. 775–833. (Soil Science Society of America: Madison, WI)

Tabatabai MA Bremner JM 1969 Use of p-nitrophenol phosphate for assay of soil phosphatase activity. Soil Biology and Biochemistry 1 301 307 doi:10.1016/0038-0717(69)90012-1

Tabatabai MA Bremner JM 1970 Arylsulphatase activity of soils. Soil Science Society of America Proceedings 34 427 429

Thorup-Kristensen K 2001 Are differences in root growth of nitrogen catch crops important for their ability to reduce soil nitrate-N content, and how can this being measured? Plant and Soil 230 185 195
doi:10.1023/A:1010306425468

Tietema A Wessel WW 1992 Gross nitrification transformations in the organic layer of acid forest ecosystems subjected to increased atmospheric nitrogen input. Soil Biology and Biochemistry 24 943 950 doi:10.1016/0038-0717(92)90021-O

Turpin JE Thompson JP Waring SA MacKenzie J 1998 Nitrate and chloride leaching in Vertosols for different tillage and stubble practices in fallow-grain cropping. Australian Journal of Soil Research 36 31 44 doi:10.1071/S97037

Webster R Payne RW 2002 Analysing repeated measurements in soil monitoring and experimentation. European Journal of Soil Science 53 1 13 doi:10.1046/j.1365-2389.2002.00408.x

Wu J Joergensen RG Pommerening B Chaussod R Brookes PC 1990 Measurement of soil microbial biomass C by fumigation-extraction—an automated procedure. Soil Biology and Biochemistry 22 1167 1169 doi:10.1016/0038-0717(90)90046-3

Zelles L 1997 Phospholipid fatty acid profiles in selected members of soil microbial communities. Chemosphere 35 275 294 doi:10.1016/S0045-6535(97)00155-0

Zelles L 1999 Fatty acid patterns of phospholipids and lipopolysaccharides in the characterization of microbial communities in soil: a review. Biology and Fertility of Soils 29 111 129 doi:10.1007/s003740050533

Zelles L Bai QY 1993 Fractionation of fatty acids derived from soil lipids by solid phase extraction and their quantitative analysis by GC-MS. Soil Biology and Biochemistry 25 495 507 doi:10.1016/0038-0717(93)90075-M

Zogg GP Zak DR Ringelberg DB MacDonald NW Pregitzer KS White DC 1997 Compositional and functional shifts in microbial communities due to soil warming. Soil Science Society of America Journal 61 475 481



Export Citation Cited By (24)