Microbial and microfaunal community structure in cropping systems with genetically modified plants

Soils from field sites at Foulum (DK), Narbons (FR) and Varois (FR) planted with genetically modified maize expressing either the insecticidal Bacillus thuringiensis protein (Bt) or herbicide tolerance (HT), as described elsewhere in this volume, were analysed for nematodes, protozoa and microbial community structure. These analyses were mirrored in single-species testing and in mesocosm experiments, and were coordinated with field samples taken for microarthropods, enchytraeids and earthworms so allowing for cross-comparison and a better understanding of the results observed in the field. Over the first 2 years of the field experiments (in 2002 and 2003), the effect of Bt-maize was within the normal variation expected in these agricultural systems. Sampling in 2004 and 2005 was expanded to include the effects of tillage (i.e. reduced tillage versus conventional tillage) and also the use of HT-maize. Tillage had major effects regardless of soil type (Varois or Foulum), with reduced-tillage plots having a greater abundance of microfauna and a different microbial community structure (measured both by phospholipid fatty-acid analysis (PLFA) and by community-level physiological profiling (CLPP)) from conventionally tilled plots. Grass, as a contrasting cropping system to maize, also had an effect regardless of soil type and resulted in greater microfaunal abundance and an altered microbial community structure. Differences in crop management, which for the Bt-maize was removal of the insecticide used to control European corn borer and for HT-maize was a change in herbicide formulation, were only tested at single sites. There were differences in microbial community structure (CLPP but not PLFA) and sporadic increases in protozoan abundance under the Bt-crop management. The HT-maize cropping system, which covered a shorter period and only one site, showed little change from the conventional system other than an altered microbial community structure (as measured by PLFA only) at the final harvest. The Bt-trait had a minimal impact, with fewer amoebae at Foulum in May 2003, fewer nematodes at Foulum in May 2004 but more protozoa at Varois in October 2002 and an altered microbial community structure (PLFA) at Foulum in August 2005. These were not persistent effects and could not be distinguished from varietal effects. Based on the field evaluations of microfauna and microorganisms, we conclude that there were no soil ecological consequences for these communities associated with the use of Bt- or HT-maize in place of conventional varieties. Other land management options, such as tillage, crop type and pest management regime, had significantly larger effects on the biology of the soil than the type of maize grown.     

Diversity and function of decomposer fungi from a grassland soil

Despite the substantial interest to ecologists of the relationship between species diversity and ecosystem functioning, little is known about how the high species richness of decomposer (saprotrophic) fungi and their relative frequencies of occurrence influence the decomposition of organic matter. Three experiments were conducted to test the ability of culturable saprotrophic fungal isolates to utilise a range of artificial and more natural substrates that occur in organic matter, with the aims of (1) characterising the functional potential of ‘common’ and ‘occasional’ taxa in an upland grassland soil and (2) determining whether there was a high degree of apparent functional redundancy in these communities. ‘Function’ was defined as the ability of a fungal isolate to utilise broad categories of substrates (e.g. sugars, cellulose, lignin) that occur in organic matter and which change in proportion during decomposition. The terms ‘common/abundant/frequent’ and ‘occasional/infrequent’ usually referred here to the frequencies of occurrence of taxa estimated using Warcup soil plates. Accepting the difficulties of sampling fungi in soil, this appeared to be the most useful isolation method to produce a general picture of the microfungal community with an estimate of frequency of occurrence for every taxon obtained, and to provide cultures for use in function tests. The influence of this technique on the interpretation of the results is discussed.Forty-eight fungal isolates, obtained from an upland grassland in Roxburghshire, UK, were selected to cover the most ‘abundant’ taxa and a range of ‘occasionals’. Pure cultures of anamorphic fungi and members of the Zygomycota, Ascomycota and Basidiomycota were tested. Although there was apparently a high degree of functional redundancy (equivalence) in assemblages of culturable decomposer fungi, with ‘frequent’ and ‘infrequent’ taxa largely utilising the same substrates, the ‘infrequent’ taxa played important roles in decomposition. ‘Infrequent’ microfungi tested were potentially more active in decomposition than the ‘frequent’ taxa, i.e. several had a higher overall activity, were able to utilise a wider range of substrates and were more combative than the ‘abundant’ taxa. When ‘abundant’ and ‘occasional’ taxa from the same putative guild were inoculated together on grass litter, there was slight evidence of ‘positive’ indirect effects on decomposition and cellulose degradation. Some ‘negative’ effects on lignin degradation, probably as a result of combat, were observed.It is possible that the ‘occasional’ taxa increased the temporal resilience of the ecosystem process of decomposition, and were ‘waiting in the wings’ to replace the abundant taxa. Nevertheless, greater functional diversity could be associated with the uncultured taxa not studied here.     

Enhanced biological cycling of phosphorus increases its availability to crops in low-input sub-Saharan farming systems

Many soils in sub-Saharan Africa, which are farmed by smallholders, are P deficient and highly P fixing. Furthermore, P inputs supplied as farmyard manure (FYM) or inorganic P fertilizer are normally too small to replace P offtakes by crops. Consequently most soils are in a negative P balance, which is reflected in small, and often declining, crop yields. The obvious solution of simply applying adequate P is seldom an option due to shortages of manure, which is usually low in nutrients in any case, and the high cost of inorganic P fertilizer relative to the likely cash value of the harvest. Our aim was to see if we could devise practical methods to increase soil P availability in this situation and to investigate the mechanisms involved. Two approaches were adopted. Firstly, to attempt to saturate the P-fixing sites in the soils by applying a large annual application of P (75 kg P ha⁻¹), which should serve for several seasons. Secondly, to attempt to keep the fertilizer P in biological forms by supplying fertilizer P and cattle manure (FYM) in combination. Here, the aim was to promote the cycling of P through the soil microbial biomass and associated metabolite pools, with the expected result of decreasing P fixation and increased plant availability of this P. These treatments were investigated using two field sites on smallholder farms in Kenya: one, considered a ‘high P fixing’ soil at Malava (Kakamega District) and one considered a ‘low P fixing’ soil at Mau Summit (Nakuru District). The following treatments were applied in 1997 and 1998: nil; 75 kg P ha⁻¹ as super phosphate (P); 25 kg P ha⁻¹; FYM at 1.9 t ha⁻¹ dry matter; FYM+25 kg P ha⁻¹. All treatments also received 100 kg inorganic N ha⁻¹. Maize was the test crop. There was no significant correlation in either year at either site between soil P, measured as NaHCO₃-extractable P, resin P or NaOH-extractable P and maize yield. However, the different soil P fractions were closely correlated with each other. Yields at the high P rate (75 kg ha⁻¹y⁻¹) were often little better than the control. There was, however, a significant positive relationship (P<0.05) between soil microbial biomass P and crop yield, again at both sites and in both years. The treatment giving the best yield and the largest biomass P was always FYM+P. Our results indicate that the combined use of organic and inorganic fertilizers in these low input systems may promote increased biological cycling, enhanced availability and consequently improved plant uptake of soil and fertiliser P, to the advantage of the small scale farmer. The results also indicate that biomass P measurements may provide a better indicator of soil P availability in these soils than some more conventional chemical extractants. However, both findings require further evaluation.     

Microbial immobilisation and turnover of N labelled substrates in two arable soils under field and laboratory conditions

Microbial biomass N dynamics were studied under field and laboratory conditions in soils of high yield (HY) and low yield (LY) areas in an agricultural field. The objective of the study was to determine the size and activity of soil microbial biomass in the soils of the different yield areas and to compare these data obtained under field and laboratory conditions. Soils were amended with ¹⁵N labelled mustard (Sinapis alba) residues (both experiments) and labelled nitrate (laboratory only) at 30 μg N g⁻¹ dry soil. Soil microbial biomass (SMB) N, mineral N (N_min) and total N content was monitored both in the field and in the laboratory. N₂O efflux was additionally measured in laboratory treatments. Isotope ratios were determined for SMB in both experiments, for all other parameters only in the laboratory treatments. In the laboratory less amounts of added substrate N were immobilised by the SMB in HY soils compared to LY soils, whereas in the field immobilisation of added N by SMB was higher in HY soils initially and slightly lower after 40 days of incubation. Calculated turnover times in the laboratory nitrate, laboratory mustard and field mustard amendments were 0.18, 0.27 and 0.74 years (HY) and 0.22, 0.61 and 1.01 years (LY), respectively. The turnover times of added substrate N always showed the trend to be faster in HY soils compared to LY soils. A faster turnover of nutrients in the HY soils may involve a better nutrient supply of the plants, which coincides with the higher agricultural yield observed in these areas.     

Carbon fluxes in soil food webs of increasing complexity revealed by C labelling and C natural abundance

Soil food webs are mainly based on three primary carbon (C) sources: root exudates, litter, and recalcitrant soil organic matter (SOM). These C sources vary in their availability and accessibility to soil organisms, which could lead to different pathways in soil food webs. The presence of three C isotopes (¹²C, ¹³C and ¹⁴C) offers an unique opportunity to investigate all three C sources simultaneously. In a microcosm experiment we studied the effect of food web complexity on the utilization of the three carbon sources. We choose an incomplete three factorial design with (i) living plants, (ii) litter and (iii) food web complexity. The most complex food web consisted of autochthonous microorganisms, nematodes, collembola, predatory mites, endogeic and anecic earthworms. We traced C from all three sources in soil, in CO₂ efflux and in individual organism groups by using maize grown on soil developed under C₃ vegetation and application of ¹⁴C labelled ryegrass shoots as a litter layer. The presence of living plants had a much greater effect on C pathways than food web complexity. Litter decomposition, measured as ¹⁴CO₂ efflux, was decreased in the presence of living plants from 71% to 33%. However, living plants increased the incorporation of litter C into microbial biomass and arrested carbon in the litter layer and in the upper soil layer. The only significant effect of food web complexity was on the litter C distribution in the soil layers. In treatments with fungivorous microarthropods (Collembola) the incorporation of litter carbon into mineral soil was reduced. Root exudates as C source were passed through rhizosphere microorganisms to the predator level (at least to the third trophic level). We conclude that living plants strongly affected C flows, directly by being a source of additional C, and indirectly by modifying the existing C flows within the food web including CO₂ efflux from the soil and litter decomposition.     

Can P NMR spectroscopy be used to indicate the origins of soil organic phosphates?

The relationship between organic P status of 4 soils, 20 microorganisms isolated from these soils (2 bacteria and 3 fungi for each soil) and 13 dominant plant species of typical natural ecosystems of these soils was evaluated. The soils used were represented by two pairs with different ratios of monoester and diester P, and of DNA and other diester P. A Dystric Podzoluvisol and an alpine Umbric Leptosol were characterized by a relatively high proportion of diester P including much DNA P, while a Calcic Chernozem and subalpine Umbric Leptosol had lower proportion of diesters containing relatively less DNA P. The proportions of P compounds in bacteria and plants were very similar on average, based on the monoester to diester P ratio and on the proportions of different diesters in alkaline extract, whereas fungi contained considerably higher proportions of monoesters and polyphosphates, and a higher proportion of phospholipids in the diester fraction. The results showed that the P_org composition of NaOH extracts from different soils was more similar to the composition of extracts from different groups of microorganisms. There was no clear correspondence between soil and microbial diester P proportion and composition. A high proportion of polyphosphate P including pyrophosphate P in soil extracts indicates a significant contribution of fungal P compounds in the soil while the monoester to diester P ratio, and DNA to non-DNA P ratio should be used with caution to interpret the origins of soil P_org. The relative contributions of microorganisms and plants to monoester and diester P in soils is only partially understood.     

添加硝化抑制剂DMPP对红壤水稻土硝化作用及微生物群落功能多样性的影响

通过室内培育试验,研究了不同施氮水平下添加硝化抑制剂(DMPP)处理对红壤水稻土NH4+-N、NO3–-N含量、微生物生物量碳及微生物群落功能多样性的影响。结果表明:56天培养期内,不同处理的NH4+-N含量总体呈下降趋势,而NO3–-N含量呈上升趋势。随施氮水平提高,培养期内NH4+-N平均含量从0 mg/kg处理的24.10 mg/kg增加到400 mg/kg处理的412.10 mg/kg,NO3–-N平均含量从0 mg/kg处理的41.88 mg/kg增加到400 mg/kg处理的99.83 mg/kg。添加DMPP显著抑制硝化作用进行,抑制效果随施氮量增加而提高,400 mg/kg施氮水平下,添加DMPP硝化率和硝化速率比不添加DMPP处理分别下降了29.0%和44.3%,下降幅度远大于其他施氮水平处理。施氮水平也影响土壤微生物生物量碳和微生物群落功能多样性。施氮量从0 mg/kg增加到400 mg/kg,土壤微生物生物量碳下降了12.5%,AWCD值下降了78.4%,Shannon指数下降了22.3%;与不添加DMPP处理相比,添加DMPP处理的土壤微生物生物量、AWCD值、Shannon指数分别提高了2.1%、23.9%、7.8%,尤其在400 mg/kg施氮水平下,提高的幅度更加明显。     

Cover crop effect on soil carbon fractions under conservation tillage cotton

Cover crops may influence soil carbon (C) sequestration and microbial biomass and activities by providing additional residue C to soil. We examined the influence of legume [crimson clover (Trifolium incarnatum L.)], nonlegume [rye (Secale cereale L.)], blend [a mixture of legumes containing balansa clover (Trifolium michelianum Savi), hairy vetch (Vicia villosa Roth), and crimson clover], and rye + blend mixture cover crops on soil C fractions at the 0–150 mm depth from 2001 to 2003. Active fractions of soil C included potential C mineralization (PCM) and microbial biomass C (MBC) and slow fraction as soil organic C (SOC). Experiments were conducted in Dothan sandy loam (fine-loamy, kaolinitic, thermic, Plinthic Kandiudults) under dryland cotton (Gossypium hirsutum L.) in central Georgia and in Tifton loamy sand (fine-loamy, siliceous, thermic, Plinthic Kandiudults) under irrigated cotton in southern Georgia, USA. Both dryland and irrigated cotton were planted in strip tillage system where planting rows were tilled, thereby leaving the areas between rows untilled. Total aboveground cover crop and cotton C in dryland and irrigated conditions were 0.72–2.90 Mg C ha⁻¹ greater in rye + blend than in other cover crops in 2001 but was 1.15–2.24 Mg C ha⁻¹ greater in rye than in blend and rye + blend in 2002. In dryland cotton, PCM at 50–150 mm was greater in June 2001 and 2002 than in January 2003 but MBC at 0–150 mm was greater in January 2003 than in June 2001. In irrigated cotton, SOC at 0–150 mm was greater with rye + blend than with crimson clover and at 0–50 mm was greater in March than in December 2002. The PCM at 0–50 and 0–150 mm was greater with blend and crimson clover than with rye in April 2001 and was greater with crimson clover than with rye and rye + blend in March 2002. The MBC at 0–50 mm was greater with rye than with blend and crimson clover in April 2001 and was greater with rye, blend, and rye + blend than with crimson clover in March 2002. As a result, PCM decreased by 21–24 g CO₂–C ha⁻¹ d⁻¹ but MBC increased by 90–224 g CO₂–C ha⁻¹ d⁻¹ from June 2001 to January 2003 in dryland cotton. In irrigated cotton, SOC decreased by 0.1–1.1 kg C ha⁻¹ d⁻¹, and PCM decreased by 10 g CO₂–C ha⁻¹ d⁻¹ with rye to 79 g CO₂–C ha⁻¹ d⁻¹ with blend, but MBC increased by 13 g CO₂–C ha⁻¹ d⁻¹ with blend to 120 g CO₂–C ha⁻¹ d⁻¹ with crimson clover from April 2001 to December 2002. Soil active C fractions varied between seasons due to differences in temperature, water content, and substrate availability in dryland cotton, regardless of cover crops. In irrigated cotton, increase in crop C input with legume + nonlegume treatment increased soil C storage and microbial biomass but lower C/N ratio of legume cover crops increased C mineralization and microbial activities in the spring.     

Relationships between microbial biomass and dissipation of 2,4-D and dicamba in soil

A study was conducted to evaluate relationships between microbial biomass and the dissipation of 2,4-D (2,4-dichlorophenoxy acetic acid) and dicamba (2-methoxy-3,6-dichlorobenzoic acid) in soil. We hypothesized that the size of the microbial biomass should be a strong predictor of the pesticide degradation capacity of a particular soil. Soils with a high microbial biomass should have relatively high levels of general microbial activity and should support a diversity of degradation pathways. In this study, we quantified the degradation of 2,4-D and dicamba in a range of soils with different concentrations of microbial biomass. The herbicides 2,4-D and dicamba were added to similar soils collected from five different land use types (home lawn, cornfield, upland hardwood forest, wetland forest, and aquifer material) and incubated for 80 days under laboratory conditions. Herbicide residue and microbial biomass (C and N) analyses were performed 5, 10, 20, 40, and 80 days following herbicide application. Microbial biomass-C and -N and soil organic matter content were positively correlated with dissipation of 2,4-D and dicamba. The results suggest that there are relationships between the size of the soil microbial biomass and the herbicide degradation capacity of an ecosystem. These relationships may be useful for developing approaches for evaluating and predicting the fate of pesticides in different ecosystems.     

Influence of temperature on CO2 evolution,microbial biomass C and metabolic quotient during the decomposition of two humic forest horizons

The decomposition of the litter layer and the humic mineral horizon from a beech forest site was studied at temperatures of 5, 12, and 22°C for both substrates and additionally at 32°C for beech litter. Weight losses, basal and substrate-induced CO₂ production, and the extractable biomass C were monitored periodically during a 2-year incubation period. Weight losses and microbial activity were controlled by substrate quality and temperature. No significant differences were found between 5 and 12°C in decomposition, biomass C, and the metabolic quotient in the humic mineral horizon. The decay of beech litter and the humic mineral horizon was highest at 22°C but was faster in the litter material by a factor of 2.9 on average. In the glucose-amended samples, the relationship among the CO₂-C fluxes was 1:1:2:3 at temperatures of 5, 12, 22, and 32°C in the litter layer, and 1: 2: 2.4 at 5, 12, and 22°C in the A horizon, respectively. The microbial activity in the humic mineral horizon was only 2–11% of that in the litter layer. The level of biomass C remained constant over 1 year and no significant differences were obtained from the 12 and 22°C treatments in the litter layer.