Biol Fertil Soils (2000) 31 : 78–84 Q Springer-Verlag 2000 ORIGINAL PAPER G.D. Bending 7 C. Putland 7 F. Rayns Changes in microbial community metabolism and labile organic matter fractions as early indicators of the impact of management on soil biological quality Received: 7 April 1999 Abstract Changes to the metabolic profiles of soil microbial communities could have potential for use as early indicators of the impact of management or other perturbations on soil functioning and soil quality. We compared the relative susceptibility to management of microbial community metabolism with a number of soil organic matter (OM) and microbial parameters currently used as indicators of changes in soil biological quality. Following long-term cereal cropping, plots were subjected to a 16-month treatment period consisting of either a mixed cropping sequence of vetch, spring barley and clover or a continuous grass-clover ley which was periodically mown and mulched. The treatments had no effect on soil biomass N or respiration of microbial populations inoculated into Biolog Gram negative (GN) plates. After 16 months there were no management-induced changes to total OM, light-fraction OM C and N, labile organic N or water-soluble carbohydrates. However, patterns of substrate utilization by the soil microbial population following inoculation into Biolog GN plates were found to be highly sensitive to management practice. In the mixed cropping sequence, substrate utilization changed markedly following plough-in of the vetch crop, with a smaller change occurring after harvesting of the barley. In the ley treatment, substrate utilization was not affected until the onset of mowing, when the pattern changed to become similar to that in the mixed cropping sequence. Metabolic diversity of the Biolog-culturable microbial G.D. Bending (Y) 7 C. Putland Department of Soil and Environmental Sciences, Horticulture Research International, Wellesbourne, Warwick CV35 9EF, UK e-mail: gary.bending6hri.ac.uk Tel.: c44-1789-470382 Fax: c44-1789-470552 F. Rayns Henry Doubleday Research Association, Ryton-on-Dunsmore, Coventry CV8 3LG, UK population was increased by the ley treatment, but was not affected by the cropping sequence. We conclude that patterns of microbial substrate utilization and metabolic diversity are more sensitive to the effects of management than are OM and biomass pools, and therefore have value as early indicators of the impacts of management on soil biological properties, and hence soil quality. Key words Biolog substrate-utilization patterns 7 Microbial metabolic diversity 7 Light-fraction organic matter 7 Microbial biomass 7 Agricultural management practices Introduction The quality of a soil is central to determining the sustainability and productivity of above-ground plant communities (Doran et al. 1994). Recently, greater environmental awareness has led to recognition of the need to maintain and enhance the quality of soil (Doran et al. 1994). This has highlighted the need for a greater understanding of the factors which contribute to soil quality, so that more reliable methods of assessment can be made, and in order to identify factors which are particularly sensitive to change. These could be used to provide early indications of the impacts of perturbations on soil quality (Trasar-Cepeda et al. 1998). While the chemical characteristics of a soil make a significant contribution to its quality, and may determine the maximum quality of a particular soil (Hassink 1997), it is the biological and biochemical components of soil quality which are most susceptible to change, and therefore to degradation by human activities. The most widely used biochemical indicator of soil quality is organic matter (OM) content. Soil OM (SOM) is crucial for sustaining crop production in agricultural soils. In addition to providing a background turnover of nutrients to drive plant growth (Jenkinson 1981), SOM also contributes to the maintenance of soil 79 structural properties which are necessary for plant growth and which prevent erosion (Oades 1984). However, changes in the amounts and characteristics of gross SOM pools occur very slowly, and long-term experiments over decades are needed to determine the impact of management practices or other perturbations on SOM dynamics (Beare et al. 1994; Ladd et al. 1994). SOM is highly heterogeneous and consists of a variety of different fractions which have various origins and functional roles in the soil (Stevenson 1994). A number of SOM fractions appear to be more labile than the gross SOM pool, with the result that changes in these pools have potential to provide an early indication of the impacts of management or environmental stress on soil quality. These pools include labile organic N, lightfraction OM (LFOM) and water-soluble carbohydrates. Labile organic N and LFOM are considered to govern patterns of N mineralization in many soils (Bonde and Roswall 1987; Janzen et al. 1992; Sierra 1996), while the carbohydrate pool, especially that linked to the heavy fraction OM, plays a role in the aggregation of soil particles, which determines soil structural properties (Oades 1984). The effect of management practices on SOM is largely mediated by the soil microbial community, and the C and N content of the biomass is also viewed as an indicator of soil quality (Rice et al. 1996). A number of techniques, including phospholipid fatty acid analysis (Zelles et al. 1992) and patterns of substrate utilization (Garland and Mills 1991), have been used to describe the diversity and structure of soil microbial populations. Since these techniques measure the profiles and activities of communities directly involved in SOM dynamics, they could have great value for the characterization of soil quality. Soil labile N and carbohydrate pools, and the C and N content of the soil microbial biomass can respond rapidly to changes in management practices and climate (Duxbury and Nkambule 1994; Kaiser and Heinmeyer 1993; Roberson et al. 1995; Rice et al. 1996). However, the dynamics of LFOM have been investigated only in soils subjected to long-term differences in management practice, and the potential of this pool to act as an early indicator of the impact of management on soil quality is not known. Further, the impacts of management on the dynamics of the labile SOM pools have largely been determined in separate studies over widely different timescales. Similarly, soil microbial diversity measurements have been most extensively used to monitor changes induced by long-term management practices or to investigate differences between soil communities from widely different habitats (Zak et al. 1994; Bossiq and Scow 1995). The aim of this study was to investigate the susceptibility of labile OM pools, and the size, metabolic profiles and diversity of the soil microbial community, to short-term changes in management practice, in order to compare the relative value of changes in these parame- ters as early indicators of the impacts of management on soil quality. Materials and methods Site details Measurements were made on treatments included in an experimental conversion of a 12-ha area of farmland from conventional to organic production, at HRI Wellesbourne, Warwickshire. The site is on a sandy loam of the Wick series, with 14% clay and a pH of 5.9. A detailed description of the soil is given in Whitfield (1974). The site had been under conventionally managed cereals for at least 20 years prior to the initiation of the study. Experimental design The treatments were established in August 1996. Following harvest of a winter wheat (Triticum aestivum L) crop the soil was ploughed to 20 cm depth and harrowed. Each treatment consisted of a 1.5-ha area divided into 6 sub-plots. Treatment 1 had a continuous cover of a rye grass (Lolium perenne L)-red clover (Trifolium pratense L) ley, which was mown to 2 cm height and mulched at monthly intervals from April–August 1997. A total dry weight biomass of 2.4 t ha –1 was mulched over this period. Treatment 2 was under winter vetch (Vicia sativa L) from August 1996 until February 1997. The vetch was then ploughed-in to a depth of 20 cm and the plot harrowed and sown with spring barley (Hordeum vulgare L) and undersown with white clover (Trifolium repens L). The barley crop was harvested in August 1997, and the white clover left to regenerate. The total dry weight biomass of shoot and root materials ploughed-in over the period studied was 3.6 t ha –1. The plots received no addition of fertilizer or pesticide for the duration of the experiment. Soil sampling Soils were sampled in August 1996, April 1997, and December 1997. From each sub-plot, 20 cores were taken with a 2.5-cmdiameter steel auger from the 0 to 30-cm layer. The cores were pooled and passed through a 3-mm sieve. Soil conditioning Soils were pre-conditioned prior to the measurement of qualitative characteristics, in order to avoid any effects of environmental variables such as temperature and moisture content. In this way, stable changes developing as a consequence of the management practices could be monitored. Soil samples were each moistened to a matric potential of P250 kPa. Samples (200 g fresh weight) were placed into 150-ml polystyrene beakers, and incubated at 15 7C for 14 days inside 15-l containers. Moist air was continuously passed through the containers to ensure that an aerobic atmosphere persisted. Microbial community metabolic profiles Substrate-utilization patterns by the soil microbial population were determined using Biolog Gram negative (GN) microplates (Biolog, California) by a procedure adapted from Garland and Mills (1991). Each plate contains 95 separate sole C sources and a blank well. The C sources include amino acids, carbohydrates, carboxylic acids and polymers, together with a number of miscellaneous compounds. The rate of utilization of the C sources is indicated by the reduction of tetrazolium, a redox indicator dye, which changes from colourless to purple. 80 Soil (5 g fresh weight) was mixed with 50 ml autoclave-sterilized 0.85% w/v NaCl solution and shaken for 30 min, and then centrifuged at 150 g for 2 min to remove larger suspended soil particles. A 2-ml volume of the supernatant was diluted with 18 ml NaCl solution, and 0.15 ml inoculated into each microplate well. The absorbance of wells at 590 nm was measured using a microplate reader. Plates were placed into plastic bags, and incubated at 20 7C in the dark. Absorbance in the microplates was re-measured after a 72-h incubation, at which point average well-colour development (AWCD) had reached approximately 0.4 absorbance units. For each well, the increase in absorbance over 72 h was divided by the AWCD of the microplate (Garland 1996a). Numbers of culturable bacteria were determined by diluting soil from 10 –2 to 10 –5 using 0.85% w/v NaCl solution, and inoculating 1 ml into 19 ml nutrient agar. The plates were incubated at 20 7C, and bacterial colonies counted after 6 days. Table 1 Effect of management on substrate richness, substrate evenness and Shannon’s diversity index for microbial community utilization of Biolog Gram negative microplate substrates. Means followed by different letters are significantly different (P~0.05) Treatment Substrate richness Substrate evenness Shannon’s diversity index Treatment 1 (grass-clover ley) August 1996 April 1997 December 1997 80.3 a 81.3 a 82.3 a 0.925 a 0.922 a 0.943 b 4.05 a 4.05 a 4.16 b Treatment 2 (crop sequence) August 1996 April 1997 December 1997 82.5 a 83.6 a 80.8 a 0.925 a 0.936 a 0.931 a 4.08 a 4.14 a 4.09 a Microbial biomass and SOM characteristics Microbial biomass N was determined by the fumigation-extraction method (Joergensen and Brookes 1990). Ninhydrin-N released on fumigation was converted to microbial N using a conversion factor of 3.1 (Amato and Ladd 1988). Total OM C and N were determined at the beginning and end of the experiment using an automated C/N analyser (CN-2000; Leco, Mich.). The LFOM content was determined by the method of Strickland and Sollins (1987). The total C and N content of LFOM was determined using the automated C/N analyser. Hot water-soluble carbohydrates were extracted by the method of Brink et al. (1960). Carbohydrates were determined by a phenol-H2SO4 assay using glucose standards (Dubois et al. 1956). Labile organic N was determined by measuring net N mineralization potential during the 2-week conditioning step (Anderson – and Ingram 1993). Soil mineral N (NH c 4 and NO 3) was determined before and following incubation using an EnviroFlow 5012 flow injection system (Tecator, Sweden). The mineralization potential was determined by subtracting mineral N present before incubation from that present following incubation. Statistical analysis T-tests were conducted to determine if there were significant changes to OM and biomass between treatments and within treatments over time. Biolog substrate-utilization patterns were analysed according to Zak et al. (1994) to give substrate richness (the number of substrates utilized), substrate evenness (the distribution of colour development between the substrates), and Shannon’s diversity index. Patterns of utilization of all Biolog substrates, and those classed as amino acids, carbohydrates, carboxylic acids and polymers, were analysed by principal component analysis (PCA), using the statistical program Genstat. Results Microbial community metabolic profiles There were no differences in substrate richness between the treatments, and this parameter did not change over time in either treatment (Table 1). In the crop sequence, there were no changes to substrate evenness or diversity over time. However, in the ley treatment, both evenness and diversity increased significantly between April 1997 and December 1997. PCA of substrate utilization for all substrates demonstrated that the communities in the two treatments were very similar at the beginning of the experiment (Fig. 1a) but that patterns of metabolism diverged with the imposition of the different management practices. There was a shift in the pattern of substrate utilization along PC 2, which was similar in the two treatments, but which occurred in April 1997 in treatment 2, and which was delayed until December 1997 in treatment 1. The pattern of substrate utilization in treatment 2 altered slightly between April 1997 and December 1997, so that the two treatments had distinctly different patterns of substrate utilization at December 1997. When the amino acids (Fig. 1b) carbohydrates (Fig. 1c) and polymer (Fig. 1d) components of the Biolog plates were analysed by PCA separately, the relative distribution of the treatments were very similar to when all substrates were analysed together (Fig. 1a). In contrast, patterns of utilization of carboxylic acids (Fig. 1e) showed clear changes in substrate use occurring in the ley between August 1996 and April 1997, while there was no difference in carboxylic acid utilization between the two treatments at December 1997. Microbial biomass and SOM characteristics There were no significant differences in biomass N or AWCD of Biolog plates between or within the treatments over the course of the study, with the parameters remaining at 14.5 mg N g –1 (dry weight) soil (SEM, B0.5) and 0.4 absorbance units (SEM, B0.01) respectively. There were no changes to the whole SOM or LFOM C and N content within or between the treatments over the course of the experiment, with C remaining at 8600 (SEMB100) and 460.4 (SEMB17.1) mg g –1 (dry weight) soil in the whole SOM and LFOM respectively, and N remaining at 960 (SEMB10) and 21.8 (SEMB0.7) mg g –1 (dry weight) soil in the whole SOM and LFOM respectively. 81 Fig. 1a–e. Principal component (PC) analysis ordination plot for Biolog substrate utilization in the treatments over time. a All substrates, b amino acids, c carbohydrates, d carboxylic acids, e polymers. Solid symbols represent treatment 1, open symbols represent treatment 2, bars represent BSEM along each PC axis. August 1996, April 1997, D December 1997 Water-soluble carbohydrates Soil mineral N and N mineralization potential There was no change in the water-soluble carbohydrate content in either treatment between August 1996 and April 1997 (Table 2). However, in both treatments this pool declined by approximately 40% between April and December 1997. At the beginning of the experiment, the soil mineral N content was the same in both treatments (Table 3). There was little change to soil mineral N in the ley over the course of the experiment. However, following plough-in of the vetch there was a fourfold increase in soil mineral N in the crop sequence. This was followed by a decline to the initial level by December 1997. There was no significant difference in mineralization 82 Table 2 Effect of management on the soil water-soluble carbohydrate pool. Figures in parentheses give BSEM. Means followed by different letters are significantly different (P~0.05). dw Dry weight Treatment 1 (grass-clover ley) Carbohydrate [mg g –1 (dw) soil] Treatment 2 (crop sequence) August 1996 April 1997 December 1997 August 1996 April 1997 December 1997 250 a (4) 261 a (19) 162 b (3) 222 ac (11) 212 c (6) 126 d (6) Table 3 Effect of management on soil mineral N and N mineralization potential. Figures in parentheses give BSEM. Means followed by different letters are significantly different (P~0.05) Treatment 1 (grass-clover ley) Soil mineral N [mg N g –1 (dw) soil] N mineralization potential [mg N g –1 (dw) soil] Treatment 2 (crop sequence) August 1996 April 1997 December 1997 August 1996 April 1997 December 1997 5.8 a (0.5) 3.3 a (0.8) 7.2 a (2.0) –4.0 b (2.2) 3.4 a (0.7) 2.0 a (0.6) 5.3 a (0.7) 4.8 a (0.5) 20.5 b (3.5) –2.2 ab (3.2) 6.1 a (0.6) 3.2 a (0.4) potential between the two treatments at any of the sampling dates. However, in both treatments there was a significant decrease in mineralization potential between August 1996 and April 1997, resulting in net immobilization of soil mineral N in April 1997. Discussion The results demonstrated that changes in patterns of substrate utilization and metabolic diversity by the Biolog-culturable soil microbial community are more sensitive indicators of management-induced effects to soil biological properties, and hence changes in soil quality, than are gross measures of the microbial biomass and labile OM components. Changes to labile OM pools reflect the balance between synthesis and degradation of that pool by the microbial biomass. While the OM pools are all ultimately derived from plant materials, the nature of the plantderived substrates which give rise to each of the measured pools are different. Further, different groups of soil microbes are likely to govern the transformations of the different labile OM pools. The rate at which each OM pool responds to changes in management or other perturbation is likely to vary considerably between soil types and according to the nature of organic inputs. Since each of the pools has a different role in terms of soil functioning, a change in any of the measured pools could be viewed as a change in the functional quality of SOM. In order to examine soil quality dynamics effectively, a range of OM pools therefore needs to be measured to take account of the varied and overlapping functional roles of different OM pools. Despite the incorporation of fresh plant materials into both treatments, the level of LFOM did not change in our study, demonstrating that the formation of this pool was in equilibrium with its degradation. Similarly, Liang et al. (1998) found that when amounts of corn crop residues returned to the soil at harvest were altered by manipulating the fertilizer regime, there was no effect on LFOM C or N over a 3 to 11-year period. However, in the same study, LFOM C and N increased markedly within 3 years of the start of a regime in which manure was added to soil, with the increase related to the amount of OM added. This suggests that the stabilization of OM added to soil as LFOM could be related to the biochemical composition of the additions, and the capacity of the soil microbial population to adapt to new substrates. This was confirmed in laboratory incubation studies for additions of plant materials (Bending et al. 1998). The dynamics of the labile organic N and water-soluble carbohydrate pools were similar in the two treatments, with changes induced by time of year of sampling, but not management. While the plough-in of vetch in treatment 2 resulted in a flush of net N mineralization from the incorporated tissues, any residual unmineralized organic N must therefore have been resistant to decomposition, or stabilized by conversion into non-labile forms. The apparent immobilization of N in spring, which occurred in both treatments, may have resulted from the activities of the saprophytic community during growth on low C/N ratio root material arising from the senescence of old roots over winter. Management practice had no effect on soil biomass N, probably because there was no change in the total OM content, or the size of most of the labile OM pools, which could be considered to represent energy sources for the biomass. In contrast to the microbial biomass and SOM characteristics, the substrate-utilization patterns suggested that the management practices employed caused 83 changes in microbial community composition. There was no change in the Biolog-culturable microbial community of the ley soil between August 1996 and April 1997. During this period there was effectively no management-induced perturbation imposed. In vitro studies have shown that Biolog-culturable rhizosphere bacterial communities can change with the age of plants, reflecting changes in amounts and composition of exudates (Garland 1996b). However, in our study there were no changes to the Biolog-culturable microbial population as the crop aged between August 1996 and April 1997, suggesting that crop growth and age had no effect on the bulk soil microbial population. Following the addition of OM to the ley soil by mowing and mulching, the composition of the microbial community did change. Similarly, in the crop sequence, the community was altered following ploughing-in of the vetch crop. In comparison, there was only a relatively small change associated with the harvest of spring barley, presumably reflecting the lower disturbance of the soil at that time. Despite the different types of material added to soil in the treatments, and the modes by which the organic materials were incorporated, the changes in the microbial community metabolic profiles following input of organic material were remarkably similar. This could have reflected similarities in the biochemical composition of the substrates incorporated, which consisted largely of N-rich leguminous materials in both treatments. There was a greater amount of OM, and diversity of substrates, incorporated into the crop sequence than the ley. However, the fact that metabolic diversity increased in the ley, but not in the crop sequence, could have reflected the impact of soil disturbance imposed by tillage. Similarly, Lupwayi et al. (1998) found that tillage reduced the diversity of Biolog-culturable bacteria, although they found that diversity increased in a sequence of different crop types relative to continuous wheat. All the different substrate groups within the Biolog plates showed changes in patterns of oxidation by the microbial population. Carboxylic acids, in contrast to the other substrates, showed clear differences with respect to community metabolism in treatment 1 between August 1996 and April 1997, but failed to show differences between the treatments in December 1997. This suggests that carboxylic acid oxidation was modified by a portion of the Biolog-culturable community which did not contribute greatly to the oxidation of the other substrates. Smalla et al. (1998) showed that the populations which develop in Biolog plates following inoculation with soil microbial communities are largely fast-growing species adapted to high substrate concentrations, including Pseudomonas, Enterobacter, Pantoea and Salmonella. 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