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Farming system impacts on microbial activity and soil organic matter dynamics in southern Australian Mallee soils

VVSR Gupta 1, David Roget1, CW Davoren2, Rick Llewellyn2 and Anthony Whitbread2

1 CSIRO Entomology, Glen Osmond, SA 5064,
CSIRO Sustainable Ecosystems, Glen Osmond, SA 5064


Soil biological functions in southern Australian dryland cropping soils are mainly regulated by the soil moisture and amount of available carbon. Microbial activities in soil mediate the majority of processes involved with carbon and nutrient cycling and overall soil organic matter (SOM) dynamics. The main hypothesis of the Mallee Sustainable Farming Project, initiated in 1997, was that intensive cropping with high water use efficiency, limited grazing and zero tillage would increase returns of organic matter to the soil with an associated increase in beneficial microbial activity and function. We investigated the effects of intensification of cropping, crop rotations and fertiliser inputs on microbial activity, the size of the microbial biomass, nutrient availability, disease suppression and SOM dynamics. Results from eight years of field trials on light textured Mallee soils in SA, Vic and NSW indicated that management changes that increased productivity and resulted in higher microbially available C inputs were the driver for greater soil microbial activity and improved microbial functions related to nutrient cycling and disease suppression. Microbial communities in the course textured Mallee soils were particularly responsive to increased C inputs due to the low soil C levels and rapid turnover of added C as a result of the limited protection offered by these soils. There was no significant increase in total soil C after eight years, probably due to the increased microbial activity and overall C and N turnover and the limited protection offered by the coarse textured soil. Tillage generally accelerated decomposition of crop residues and SOM and overall decline in soil resource quality.

Key words

microbial biomass, carbon, catabolic diversity, tillage, particulate organic matter


Soil biological functions in southern Australian dryland cropping soils are mainly regulated by the soil moisture and amount of biologically available carbon. Crop management practices such as crop rotation, stubble retention and tillage influence the quality, quantity and location of crop residues. Stubble retention has generally been shown to maintain or increase soil organic carbon, especially when combined with reduced or zero tillage systems (Dalal and Chan, 2001). Microbial communities associated with different crop types and varieties differ in terms of composition, activity and their nutrient content (Grayston et al., 1998; Gupta et al., 2004; Bais et al., 2006). Crop rotation, therefore, influences soil biota directly by choice of crop types and indirectly by associated management practices.

Organic C enters soil through rhizodeposition and dead plant residues. Total organic C in soil is determined by the balance between inputs and losses through decomposition. Decomposition of crop residues and formation and mineralisation of soil organic matter (SOM) are influenced by soil and climatic conditions, activities of microorganisms and soil fauna (biological processes) and the quantity and quality of crop residues (resource quality) (Adl, 2003). Resource quality is generally defined in terms of C and nutrient availability to saprophytic microorganisms.

Biological processes such as decomposition, nutrient mineralisation and disease suppression are a product of the composition and activities of a variety of functional groups of soil biota. The majority of soil microbes require carbon as a source of energy therefore carbon inputs through above and below ground plant (roots) residues have a major influence on populations of biota and soil biological activities. Soil texture and soil structure both play important roles in microbial decomposition processes and influence the amounts of carbon and other nutrients released from decomposition and the potential build up of soil organic matter. Particulate organic matter (POM) is the microsite for the majority of microbial activity in soils, particularly lighter textured soils. Particulate organic matter that is encrusted with microbially produced organic compounds and soil particles during aggregate formation protect organic matter from further decomposition by controlling microbial access and activity. Disruption of aggregates due to cultivation and the subsequent release and decomposition of organic material once protected within the aggregate structure is one important mechanism by which carbon is lost from soils (Gupta and Germida, 1988; Six et al., 2000; Dalal and Chan, 2001), especially for soil types with low protection.

The low productivity in the traditional Mallee pasture-cropping systems with multiple cultivations combined with factors such as heavy grazing, fallowing and wind erosion have resulted in low returns of organic matter to the soils with subsequent limitations to microbial activities and functions. Benefits from intensive cropping and stubble retention are only likely in no-till systems with no significant soilborne diseases. In addition, conservation farming operations help control wind erosion through improved soil aggregation and better soil cover (Leys et al. 1996).

The Mallee Sustainable Farming Project commenced in 1997 to investigate the potential of improving Mallee farming systems in terms of productivity and profitability. The main hypothesis was that intensive cropping with high WUE, limited grazing and zero tillage would result in a substantial increase in the return of organic matter to the soil with an associated increase in microbial activity and function, which are essential for the long-term sustainability of any farming system (Figure 1). In this paper we discuss the effect of various farming systems, i.e. intensification of cropping, crop rotations and fertiliser inputs on microbial activity, the size of microbial biomass (MB), and overall soil organic C dynamics after 8 years.

Figure 1. Management of soil organic carbon and nutrient availability in the intensive cropping systems in the low-rainfall Mallee. This diagram explains the role of microbial biomass in carbon turnover and nutrient mineralization and the influence of management practices (e.g. carbon inputs and tillage). MB = Microbial biomass, POM = particulate organic matter, SOM=soil organic matter


The field trial was established at Waikerie, South Australia, (34 17’ S, 14002’ E) in 1998. The climate is Mediterranean-type, characterised by hot dry summers and a winter-dominant, average annual rainfall of only 260mm. The soil is an alkaline calcareous loamy sand, classification Um5 (Northcote et al., 1975), or alfisol (Dudal 1968). Soil chemical properties (0-10cm) at the start of the trial were pH(water) 8.6, organic C 0.68%, total N 0.05%, Colwell bicarbonate-extractable P 12 mg/kg, and CaCO3 0.4%, Clay content 6%. Surface samples collected prior to sowing each year were analysed for microbial activity and microbial biomass C and N (Gupta et al., 1994) and samples from 2006 were also analysed for catabolic profile of the microbial community (Campbell et al., 2003) and total and POM-C and N concentrations (Camberdella and Elliott, 1993). Treatments included a combination of rotation (wheat, canola and pasture and grain legumes), tillage (no-till, conventional cultivation) and fertiliser inputs (District practice and Hi-input).

Results and Discussion

Data on yield and economic performance of various farming system treatments over the trial period indicated that intensive cropping combined with the management of inputs to meet predicted potential yield estimates are better than the conventional low-input pasture-crop system. Despite the expected benefits from N-fixation through legume-rhizobium symbiosis, low grain yields from the grain legumes resulted in lower economic returns from the wheat-pulse system (Roget and Gupta, 2004).

The term ‘Microbial biomass’ (MB) refers to the entire microbial community as a single entity. MB carbon in Mallee soils ranged from 165 to 700 mg per kg soil which accounted for 2-5% of soil organic matter. Although the size of the MB is small, as it is the living component of SOM it plays a significant role in the turnover of C and nutrients and in a variety of ecosystem functions, e.g. decomposition, nutrient cycling. Results from the Mallee core trial clearly showed that MB-C, MB-N and MB-P (data not shown), in 2002, were significantly higher in high input cropping systems (both intensive and Pasture-Wheat systems) compared to traditional Pasture-Wheat (DP) systems (Table 1). MB levels in the high input Pasture-Wheat system were particularly higher after the pasture phase. The higher MB-C under Pasture-Wheat (DP) in 2006 is due to no grazing in the experimental plots in the year prior to sampling. Cultivation during the off-season resulted in a significant reduction in MB. MB fluctuated during the season and the level of nutrients in MB at the beginning of the season reflected the nutrient supplying capacity of a soil during that season.

After eight years of various cropping systems there was a significant change in the composition of microbial communities (catabolic diversity) due to the increased C inputs (intensive cropping systems different from pasture-wheat rotation) and differences in quality of C inputs (intensive Wheat rotation different from Legume-Wheat and Canola-Wheat) (data not shown). In contrast to the DD intensive cropping systems, microbial communities under Cultivated Legume-Wheat rotation were similar to that under Pasture-Wheat systems highlighting the impact of disturbance on microbial communities. Soils under DD intensive cropping systems also showed higher disease suppression potential compared to traditional DP systems.

Table 1: Microbial biomass carbon and nutrient levels in the surface soils (0-10cm) of selected treatments at Waikerie core site during 2002 (after 4 years) and 2006 (after 8 years).

Note: DP= district practice fertiliser rate comprising 10 kg P/ ha, 5 kg N/ha and cultivated; DD=direct drill; Hi= high fertiliser rate comprising 15 kg P/ha; 27 kg N/ha (N excluded for pulse crops); cult=conventional cultivation

The higher the level of soil microbial activity the greater the opportunity for nutrients (such as nitrogen and phosphorus) to be made available to plants, however synchronisation of nutrient mineralisation with plant demand is needed for efficient use of the mineralised nutrients. For example, accelerated decomposition and mineralisation due to cultivations during off-season could result in N leaching, especially under stubble burnt systems. Cropping systems that support higher levels of MB and maintain high microbial activity (e.g. high input pasture-wheat rotation and intensive cropping systems) have greater N mineralization (25-59 kg N/ha) compared to low input pasture-crop system (10-22 kg N/ha).

Soil organic matter is an important source of C (energy) and nutrients for microbial activity. It plays an important role in providing habitable pore space for the diverse range of microbial communities in soil. Research from other parts of the Australia and overseas has indicated that management practices such as stubble retention, tillage and crop rotations (in particular pasture frequency) can significantly influence the total C status and the size of different carbon pools. However the effects generally take a long time to be realised generally more than 7-10 years. Results discussed above indicate the short-term effects of management practices such as stubble retention, rotation and cultivation on the MB resulting in benefits in nutrient supply. No increase in total organic C in soil after eight years (Figure 2) and more importantly organic C declined significantly under treatments where cultivation or low-input pasture-crop rotations occurred. Organic C levels also decreased significantly in rotations with grain legumes. Data on POM indicated no significant changes in POM-C (26-34% of total C) but a significant reduction POM-N under intensive cropping systems (legume-wheat rotations). Overall C/N ratios were narrower in pasture-crop rotations (e.g. total C/N ratios <12 and POM C/N ratios <16) compared to that in intensive cropping systems (e.g. total C/N ratios >13 and POM C/N ratios >23). The different factors that can be responsible for these results include; (i) Lack of protection to SOM and crop residues in the sandy textured Mallee soils from microbial decomposition (Six et al., 2000), (ii) Disruption of aggregates and associated accelerated decomposition due to cultivation (Gupta and Germida, 1988; Dalal and Chan, 2001), (iii) The wide C/N ratio (>100) of wheat stubble contributing to the wider C/N ratio in the intensive wheat system and (iv) Higher concentration of N in legume residues that support higher microbial activity combined with lower amounts of total crop residue inputs resulted in a decline in organic C levels under grain legume-wheat rotation.

Figure 2. Soil organic C in the surface (0-10cm) soil samples collected prior to sowing during 2006 from the Waikerie core site after eight years of new farming systems. P=pasture, W=wheat, L=grain legume, C=canola

Recently there has been a growing interest in Australia to use agricultural soils for carbon sequestration. Carbon in soil is part of biological C cycle and a product of inputs through plant growth and losses by microbial activity, both are influenced by soil type, seasonal conditions and management practices. Stubble burning and export of residues contribute to losses and reduce the opportunity to increase soil C stocks. The ability to stabilise SOM is a key factor in soil C dynamics and the potential to increase soil C. Physicochemical properties inherent to soil types determine the maximum protective capacity of organic matter pools (e.g. POM) thereby affecting increases in SOM and influencing sequestration duration (West and Six, 2007). Lack of protection is one of the key elements influencing the changes in SOM in the coarse textured Mallee soils. Available evidence from other studies suggests that any increases in organic C in Australian cropping soils can only be expected at slower rates (decades or longer) and holding such increases requires continual additions of high inputs of C (Dalal and Chan, 2001; Grace, 2007; Kirkegaard et al., 2007; Umbers, 2007).


In light textured Mallee soils in SA, Vic and NSW management changes that increased productivity and resulted in higher microbially available C inputs increased soil microbial activity and improved microbial functions. The course textured Mallee soils were particularly responsive to increased C inputs due to the low soil C and rapid turnover of added C as a result of the limited protection offered by these soils. Even with improved C inputs under high input intensive cropping systems, there was no measurable increase in total soil C after eight years, probably due to the increased microbial activity and overall C and N turnover. Disturbance, in the form of tillage, accelerates decomposition of crop residues and SOM and results in an overall decline in soil resource quality. Therefore benefits from intensive cropping and stubble retention may only be realised in no-till systems. In addition, conservation farming operations are essential for controlling wind erosion.


Financial support was provided by the CSIRO, Mallee Sustainable Farming Inc and GRDC. Authors wish to thank all the technical officers involved in the long-term experiment for their efforts with field work and laboratory analysis.


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