External agricultural inputs such as mineral fertilisers, organic amendments, microbial inoculants, and pesticides are applied with the ultimate goal of maximising productivity and economic returns, while side effects on soil organisms are often neglected. We have summarised the current understanding of how agricultural inputs affect the amounts, activity, and diversity of soil organisms. Mineral fertilisers have limited direct effects, but their application can enhance soil biological activity via increases in system productivity, crop residue return, and soil organic matter. Another important indirect effect especially of N fertilisation is soil acidification, with considerable negative effects on soil organisms. Organic amendments such as manure, compost, biosolids, and humic substances provide a direct source of C for soil organisms as well as an indirect C source via increased plant growth and plant residue returns. Non-target effects of microbial inoculants appear to be small and transient. Among the pesticides, few significant effects of herbicides on soil organisms have been documented, whereas negative effects of insecticides and fungicides are more common. Copper fungicides are among the most toxic and most persistent fungicides, and their application warrants strict regulation. Quality control of organic waste products such as municipal composts and biosolids is likewise mandatory to avoid accumulation of elements that are toxic to soil organisms.

Impact of agricultural inputs on soil organisms—a review

Recent applications of biotechnology, especially genetic engineering, have revolutionized crop improvement and increased the availability of valuable new traits. A current example is the use of the insecticidal Cry proteins from the bacterium, Bacillus thuringiensis (Bt), to improve crops, known as Bt crops, by reducing injury from various crop pests. The adoption of genetically modified (GM) crops has increased dramatically in the last 11 years. However, the introduction of GM plants into agricultural ecosystems has raised a number of questions, including the ecological impact of these plants on soil ecosystems. Crop residues are the primary source of carbon in soil, and root exudates govern which organisms reside in the rhizosphere. Therefore, any change to the quality of crop residues and rhizosphere inputs could modify the dynamics of the composition and activity of organisms in soil. Insect-resistant Bt crops have the potential to change the microbial dynamics, biodiversity, and essential ecosystem functions in soil, because they usually produce insecticidal Cry proteins through all parts of the plant. It is crucial that risk assessment studies on the commercial use of Bt crops consider the impacts on organisms in soil. In general, few or no toxic effects of Cry proteins on woodlice, collembolans, mites, earthworms, nematodes, protozoa, and the activity of various enzymes in soil have been reported. Although some effects, ranging from no effect to minor and significant effects, of Bt plants on microbial communities in soil have been reported, using both culturing and molecular techniques, they were mostly the result of differences in geography, temperature, plant variety, and soil type and, in general, were transient and not related to the presence of the Cry proteins. The respiration (i.e., CO2 evolution) of soils cultivated with Bt maize or amended with biomass of Bt maize and other Bt crops was generally lower than from soils cultivated with or amended with biomass of the respective non-Bt isolines, which may have been a result of differences in chemical composition (e.g., the content of starch, soluble N, proteins, carbohydrates, lignin) between Bt plants and their near-isogenic counterparts. Laboratory and field studies have shown differences in the persistence of the Cry proteins in soil, which appear to be the result primarily of differences in microbial activity, which, in turn, is dependent on soil type (e.g., pH, clay mineral composition, other physicochemical characteristics), season (e.g., temperature, water tension), crop species (e.g., chemical composition, C:N ratio, plant part), crop management practices (e.g., till vs. no-till), and other environmental factors that vary with location and climate zones. This review discusses the available data on the effects of Cry proteins on below-ground organisms, the fate of these proteins in soil, the techniques and indicators that are available to study these aspects, and future directions.

Fate and effects of insect-resistant Bt crops in soil ecosystems

Understanding the prevalence and polymorphism of antibiotic resistance genes in soil bacteria and their potential to be transferred horizontally is required to evaluate the likelihood and ecological (and possibly clinical) consequences of the transfer of these genes from transgenic plants to soil bacteria. In this study, we combined culture-dependent and -independent approaches to study the prevalence and diversity of bla genes in soil bacteria and the potential impact that a 10-successive-year culture of the transgenic Bt176 corn, which has a blaTEM marker gene, could have had on the soil bacterial community. The bla gene encoding resistance to ampicillin belongs to the beta-lactam antibiotic family, which is widely used in medicine but is readily compromised by bacterial antibiotic resistance. Our results indicate that soil bacteria are naturally resistant to a broad spectrum of beta-lactam antibiotics, including the third cephalosporin generation, which has a slightly stronger discriminating effect on soil isolates than other cephalosporins. These high resistance levels for a wide range of antibiotics are partly due to the polymorphism of bla genes, which occur frequently among soil bacteria. The blaTEM116 gene of the transgenic corn Bt176 investigated here is among those frequently found, thus reducing any risk of introducing a new bacterial resistance trait from the transgenic material. In addition, no significant differences were observed in bacterial antibiotic-resistance levels between transgenic and nontransgenic corn fields, although the bacterial populations were different.

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Antibiotic-resistant soil bacteria in transgenic plant fields

The worldwide commercial cultivation of genetically modified (GM) crops has raised concerns about potential adverse effects on the environment resulting from the use of these crops. Consequently, the risks of GM crops for the environment, and especially for biodiversity, have been extensively assessed before and during their commercial cultivation. Substantial scientific data on the environmental effects of the currently commercialized GM crops are available today. We have reviewed this scientific knowledge derived from the past 10 years of worldwide experimental field research and commercial cultivation. The review focuses on the currently commercially available GM crops that could be relevant for agriculture in Western and Central Europe (i.e., maize, oilseed rape, and soybean), and on the two main GM traits that are currently commercialized, herbicide tolerance (HT) and insect resistance (IR). The sources of information included peer-reviewed scientific journals, scientific books, reports from regions with extensive GM crop cultivation, as well as reports from international governmental organizations. The data available so far provide no scientific evidence that the cultivation of the presently commercialized GM crops has caused environmental harm. Nevertheless, a number of issues related to the interpretation of scientific data on effects of GM crops on the environment are debated controversially. The present review highlights these scientific debates and discusses the effects of GM crop cultivation on the environment considering the impacts caused by cultivation practices of modern agricultural systems.

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Ecological impacts of genetically modified crops: ten years of field research and commercial cultivation.

Biochar addition to soil has been generally associated with crop yield increases observed in some soils, and increased nutrient availability is one of the mechanisms proposed. Any impact of biochar on soil organisms can potentially translate to changes in nutrient availability and crop productivity, possibly explaining some of the beneficial and detrimental yield effects reported in literature. Therefore, the main aim of this study was to assess the medium-term impact of biochar addition on microbial and faunal activities in a temperate soil cropped to corn and the consequences for their main functions, litter decomposition and mineralization. Biochar was added to a corn field at rates of 0, 3, 12, 30 tons ha � 1 three years prior to this study, in comparison to an annual application of 1 t ha � 1 . Biochar application increased microbial abundance, which nearly doubled at the highest addition rate, while mesofauna activity, and litter decomposition facilitated by mesofauna were not increased signif- icantly but were positively influenced by biochar addition when these responses were modeled, and in the last case directly and positively associated to the higher microbial abundance. In addition, in short- term laboratory experiments after the addition of litter, biochar presence increased NO2 þ NO3 miner- alization, and decreased that of SO4 and Cl. However, those nutrient effects were not shown to be of concern at the field scale, where only some significant increases in SOC, pH, Cl and PO4 were observed. Therefore, no negative impacts in the soil biota activities and functions assessed were observed for the tested alkaline biochar after three years of the application, although this trend needs to be verified for other soil and biochar types.

/pdf/medium-term-effects-of-corn-biochar-addition-on-soil-biota-33544wbgue.pdf

Medium-term effects of corn biochar addition on soil biota activities and functions in a temperate soil cropped to corn

Field trials were established at three European sites (Denmark, Eastern France, South-West France) of genetically modified maize (Zea mays L.) expressing the CryIAb Bacillus thuringiensis toxin (Bt), the near-isogenic non-Bt cultivar, another conventional maize cultivar and grass. Soil from Denmark was sampled at sowing (May) and harvest (October) over two years (2002, 2003); from E France at harvest 2002, sowing and harvest 2003; and from SW France at sowing and harvest 2003. Samples were analysed for microbial community structure (2003 samples only) by community-level physiological-profiling (CLPP) and phospholipid fatty acid analysis (PLFA), and protozoa and nematodes in all samples. Individual differences within a site resulted from: greater nematode numbers under grass than maize on three occasions; different nematode populations under the conventional maize cultivars once; and two occasions when there was a reduced protozoan population under Bt maize compared to non-Bt maize. Microbial community structure within the sites only varied with grass compared to maize, with one occurrence of CLPP varying between maize cultivars (Bt versus a conventional cultivar). An overall comparison of Bt versus non-Bt maize across all three sites only revealed differences for nematodes, with a smaller population under the Bt maize. Nematode community structure was different at each site and the Bt effect was not confined to specific nematode taxa. The effect of the Bt maize was small and within the normal variation expected in these agricultural systems.

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A Comparison of Soil Microbial Community Structure, Protozoa and Nematodes in Field Plots of Conventional and Genetically Modified Maize Expressing the Bacillus thuringiens is CryIAb Toxin

The effects of maize expressing the Bacillus thuringiensis Cry1Ab protein (Bt maize) on decomposition processes under three different European climatic conditions were assessed in the field. Farming practices using Bt maize were compared with conventional farming practices using near-isogenic non-Bt maize lines under realistic agricultural practices. The litter-bag method was used to study litter decomposition and nitrogen mineralization dynamics of wheat straw. After 4 months incubation in the field, decomposition and mineralization were mainly influenced by climatic conditions with no negative effect of the Bt toxin on decomposition processes.

/pdf/decomposition-processes-under-bt-bacillus-thuringiensis-2e8nlcru7i.pdf

Decomposition processes under Bt ( Bacillus thuringiensis ) maize: Results of a multi-site experiment

The effects of maize expressing the Bacillus thuringiensis Cry1Ab protein (Bt maize) on decomposition processes under three different European climatic conditions were assessed in the field. Farming practices using Bt maize were compared with conventional farming practices using near-isogenic non-Bt maize lines under realistic agricultural practices. The litter-bag method was used to study litter decomposition and nitrogen mineralization dynamics of wheat straw. After 4 months incubation in the field, decomposition and mineralization were mainly influenced by climatic conditions with no negative effect of the Bt toxin on decomposition processes. q 2005 Elsevier Ltd. All rights reserved.

Short communication Decomposition processes under Bt (Bacillus thuringiensis) maize: Results of a multi-site experiment

Agricultural studies of GM maize and the field experimental infrastructure of ECOGEN

Summary Within the ECOGEN project, long-term field experiments with genetically modified maize, Zea mays L. were conducted to study agro-ecological effects on the soil fauna and agro-economic implications of the technology. Here, we describe the studysites, experimental layout and results of agro-economic relevance. Experiments were conducted during 2002–2005 in Denmark (Foulum), northern France (Varois) and the Midi-Pyrenees region of southern France (Narbons). MON810 Bacillus thuringiensis (Bt)-varieties expressing the Cry1Ab protein, and a T25 glufosinateammonium (Basta) tolerant variety expressing the pat-gene encoding phosphinotrinacetyl-transferase were compared with near-isogenic non-Bt varieties, and conventional maize varieties. At Foulum, the maize was harvested for silage. There were no significant differences in yield between Bt-maize and a near-isogenic non-Bt variety, while a small difference in N-concentration of dry matter was detected in 1 year in a range of a measured quality parameters. Similar yield and quality were found in ploughed and reduced tillage treatments in all varieties. At Varois, the maize was harvested at ripeness and no significant differences in grain yield between Bt-maize and near-isogenic non-Bt varieties were found. These results were expected, as only Narbons harbours significant corn-borer populations. At Narbons, the number of Sesamia and Ostrinia corn-borer larvae were significantly lower in the Bt-maize than in a near-isogenic non-Bt variety and for Sesamia even less than in conventional varieties sprayed with pesticides to control corn-borer infestation. Here, Bt-maize produced a higher grain yield and grain size than a near-isogenic

SOIL ECOLOGICAL AND ECONOMIC EVALUATION OF GENETICALLY MODIFIED CROPS - ECOGEN Agricultural studies of GM maize and the field experimental infrastructure of ECOGEN

Bernard Lacroix

Papers

A Comparison of Soil Microbial Community Structure, Protozoa and Nematodes in Field Plots of Conventional and Genetically Modified Maize Expressing the Bacillus thuringiens is CryIAb Toxin

Decomposition processes under Bt ( Bacillus thuringiensis ) maize: Results of a multi-site experiment

Short communication Decomposition processes under Bt (Bacillus thuringiensis) maize: Results of a multi-site experiment

Agricultural studies of GM maize and the field experimental infrastructure of ECOGEN

SOIL ECOLOGICAL AND ECONOMIC EVALUATION OF GENETICALLY MODIFIED CROPS - ECOGEN Agricultural studies of GM maize and the field experimental infrastructure of ECOGEN