Production risk, pesticide use and GM crop technology in South Africa

Technology involving genetic modification of crops has the potential to make a contribution to rural poverty reduction in many developing countries. Thus far, pesticide-producing Bacillus thuringensis (Bt) varieties of cotton have been the main GM crops under cultivation in developing nations. Several studies have evaluated the farm-level performance of Bt varieties in comparison to conventional ones by estimating production technology, and have mostly found Bt technology to be very successful in raising output and/or reducing pesticide input. However, the production risk properties of this technology have not been studied, although they are likely to be important to risk-averse smallholders. This study investigates the output risk aspects of Bt technology by estimating two 'flexible risk' production function models allowing technology to independently affect the mean and higher moments of output. The first is the popular Just-Pope model and the second is a more general 'damage control' flexible risk model. The models are applied to cross-sectional data on South African smallholders, some of whom used Bt varieties. The results show no evidence that a 'risk-reduction' claim can be made for Bt technology. Indeed, there is some evidence to support the notion that the technology increases output risk, implying that simple (expected) profit computations used in past evaluations may overstate true benefits.

Iron Uptake and Homeostasis in Microorganisms

Preface. Iron is considered to be a minor element employed, in a variety of forms, by nearly all living organisms. In some cases, it is utilised in large quantities, for instance for the formation of magnetosomes within magnetotactic bacteria or during use of iron as a respiratory donor or acceptor by iron oxidising or reducing bacteria. However, in most cases the role of iron is restricted to its use as a cofactor or prosthetic group assisting the biological activity of many different types of protein. The key metabolic processes that are dependent on iron as a cofactor are numerous; they include respiration, light harvesting, nitrogen fixation, the Krebs cycle, redox stress resistance, amino acid synthesis and oxygen transport. Indeed, it is clear that Life in its current form would be impossible in the absence of iron. One of the main reasons for the reliance of Life upon this metal is the ability of iron to exist in multiple redox states, in particular the relatively stable ferrous (Fe2+) and ferric (Fe3+) forms. The availability of these stable oxidation states allows iron to engage in redox reactions over a wide range of midpoint potentials, depending on the coordination environment, making it an extremely adaptable mediator of electron exchange processes. Iron is also one of the most common elements within the Earth’s crust (5% abundance) and thus is considered to have been readily available when Life evolved on our early, anaerobic planet. However, as oxygen accumulated (the ‘Great oxidation event’) within the atmosphere some 2.4 billion years ago, and as the oceans became less acidic, the iron within primordial oceans was converted from its soluble reduced form to its weakly-soluble oxidised ferric form, which precipitated (~1.8 billion years ago) to form the ‘banded iron formations’ (BIFs) observed today in Precambrian sedimentary rocks around the world. These BIFs provide a geological record marking a transition point away from the ancient anaerobic world towards modern aerobic Earth. They also indicate a period over which the bio-availability of iron shifted from abundance to limitation, a condition that extends to the modern day. Thus, it is considered likely that the vast majority of extant organisms face the common problem of securing sufficient iron from their environment – a problem that Life on Earth has had to cope with for some 2 billion years. This struggle for iron is exemplified by the competition for this metal amongst co-habiting microorganisms who resort to stealing (pirating) each others iron supplies! The reliance of micro-organisms upon iron can be disadvantageous to them, and to our innate immune system it represents a chink in the microbial armour, offering an opportunity that can be exploited to ward off pathogenic invaders. In order to infect body tissues and cause disease, pathogens must secure all their iron from the host. To fight such infections, the host specifically withdraws available iron through the action of various iron depleting processes (e.g. the release of lactoferrin and lipocalin-2) – this represents an important strategy in our defence against disease. However, pathogens are frequently able to deploy iron acquisition systems that target host iron sources such as transferrin, lactoferrin and hemoproteins, and thus counteract the iron-withdrawal approaches of the host. Inactivation of such host-targeting iron-uptake systems often attenuates the pathogenicity of the invading microbe, illustrating the importance of ‘the battle for iron’ in the infection process. The role of iron sequestration systems in facilitating microbial infections has been a major driving force in research aimed at unravelling the complexities of microbial iron transport processes. But also, the intricacy of such systems offers a challenge that stimulates the curiosity. One such challenge is to understand how balanced levels of free iron within the cytosol are achieved in a way that avoids toxicity whilst providing sufficient levels for metabolic purposes – this is a requirement that all organisms have to meet. Although the systems involved in achieving this balance can be highly variable amongst different microorganisms, the overall strategy is common. On a coarse level, the homeostatic control of cellular iron is maintained through strict control of the uptake, storage and utilisation of available iron, and is co-ordinated by integrated iron-regulatory networks. However, much yet remains to be discovered concerning the fine details of these different iron regulatory processes. As already indicated, perhaps the most difficult task in maintaining iron homeostasis is simply the procurement of sufficient iron from external sources. The importance of this problem is demonstrated by the plethora of distinct iron transporters often found within a single bacterium, each targeting different forms (complex or redox state) of iron or a different environmental condition. Thus, microbes devote considerable cellular resource to securing iron from their surroundings, reflecting how successful acquisition of iron can be crucial in the competition for survival. The aim of this book is provide the reader with an overview of iron transport processes within a range of microorganisms and to provide an indication of how microbial iron levels are controlled. This aim is promoted through the inclusion of expert reviews on several well studied examples that illustrate the current state of play concerning our comprehension of how iron is translocated into the bacterial (or fungal) cell and how iron homeostasis is controlled within microbes. The first two chapters (1-2) consider the general properties of microbial iron-chelating compounds (known as ‘siderophores’), and the mechanisms used by bacteria to acquire haem and utilise it as an iron source. The following twelve chapters (3-14) focus on specific types of microorganism that are of key interest, covering both an array of pathogens for humans, animals and plants (e.g. species of Bordetella, Shigella, , Erwinia, Vibrio, Aeromonas, Francisella, Campylobacter and Staphylococci, and EHEC) as well as a number of prominent non-pathogens (e.g. the rhizobia, E. coli K-12, Bacteroides spp., cyanobacteria, Bacillus spp. and yeasts). The chapters relay the common themes in microbial iron uptake approaches (e.g. the use of siderophores, TonB-dependent transporters, and ABC transport systems), but also highlight many distinctions (such as use of different types iron regulator and the impact of the presence/absence of a cell wall) in the strategies employed. We hope that those both within and outside the field will find this book useful, stimulating and interesting. We intend that it will provide a source for reference that will assist relevant researchers and provide an entry point for those initiating their studies within this subject. Finally, it is important that we acknowledge and thank wholeheartedly the many contributors who have provided the 14 excellent chapters from which this book is composed. Without their considerable efforts, this book, and the understanding that it relays, would not have been possible. Simon C Andrews and Pierre Cornelis

A further study of the recovery and purification of surfactin from fermentation broth by membrane filtration

Surfactin is a bacterial lipopeptide produced by Bacillus subtilis and is a powerful surfactant, having also antiviral, antibacterial and antitumor properties. The recovery and purification of surfactin from complex fermentation broths is a major obstacle to its commercialization; therefore, a two-step membrane filtration process was developed using a lab scale tangential flow filtration (TFF) unit with 10 kDa MWCO regenerated cellulose (RC) and polyethersulfone (PES)membranes at three different transmembrane pressure (TMP) of 1.5 bar, 2.0 bar and 2.5 bar. Two modes of filtrations were studied, with and without cleaning of membranes prior to UF-2. In a first step of ultrafiltration (UF-1), surfactin was retained effectively by membranes at above its critical micelle concentration (CMC); subsequently in UF-2, the retentate micelles were disrupted by addition of 50% (v/v) methanol solution to allow recovery of surfactin in the permeate. Main protein contaminants were effectively retained by the membrane in UF-2. Flux of permeates, rejection coefficient (R) of surfactin and proteinwere measured during the filtrations. Overall the three different TMPs applied have no significant effect in the filtrations and PES is the more suitable membrane to selectively separate surfactin from fermentation broth, achieving high recovery and level of purity. In addition this two-step UF process is scalable for larger volume of samples without affecting the original functionality of surfactin, although membranes permeability can be affected due to exposure to methanolic solution used in UF-2.

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

The combined effect of the application of a biocontrol agent Paecilomyces lilacinus, with various practices for the control of root-knot nematodes

The effectiveness of a formulated product containing spores of the naturally occurring fungus Paecilomyces lilacinus, strain 251, was evaluated against root-knot nematodes in pot and greenhouse experiments. Decrease of second-stage juveniles hatching from eggs was recorded by using the bio-nematicide at a dose of 4 kg ha(-1), while a further decrease was recorded by doubling the dose. However, the mortality rate decreased by increasing the inoculum level. Application of P. lilacinus and Bacillus firmus, singly or together in pot experiments, provided effective control of second-stage juveniles, eggs or egg masses of root-knot nematodes. In a greenhouse experiment, the bio-nematicide was evaluated for its potential to control root-knot nematodes either as a stand-alone method or in combination with soil solarization. Soil was solarized for 15 d and the bio-nematicide was applied just after the removal of the plastic sheet. Soil solarization for 15 d either alone or combined with the use of P. lilacinus did not provide satisfactory control of root-knot nematodes. The use of oxamyl, which was applied 2 weeks before and during transplanting, gave results similar to the commercial product containing P. lilacinus but superior to soil solarization. (C) 2007 Elsevier Ltd. All rights reserved.

Explaining contradictory evidence regarding impacts of genetically modified crops in developing countries. Varietal performance of transgenic cotton in India

A study of the commercial growing of different varieties of Bacillus thuringiensis (Bt) cotton compares the performance of growing official and unofficial hybrid varieties of Bt cotton and conventional (non-Bt) hybrids in Gujarat by 622 farmers. Results suggest that the official Bt varieties (MECH 12 and MECH 162) significantly outperform the unofficial varieties. However, unofficial, locally produced Bt hybrids can also perform significantly better than non-Bt hybrids, although second generation (F-2) Bt seed appears to have no yield advantage compared to non-Bt hybrids but can save on insecticide use. Although hybrid vigour is reduced, or even lost, with F-2 seed the Bt gene still confers some advantage. The F-2 seed is regarded as 'GM' by the farmers (and is sold as such), even though its yield performance is little better than the non-GM hybrids. The results help to explain why there is so much confusion arising from GM cotton release in India.

Farm-level economic performance of genetically modified cotton in Maharashtra, India

A study of the commercial growing of Bacillus flutringiensis (Bt) cotton in India, compares the performance of over 9,000 Bt and non-Bt cotton farm plots in Maharashtra over the 2002 and 2003 seasons. Results show that since their commercial release in 2002, Bt cotton varieties have had a significant positive impact on average yields and on the economic performance of cotton growers. Regional variation showed that, in a very few areas, not all farmers had benefited from increased performance of Bt varieties.

An ex-ante evaluation of the economic impact of Bt cotton adoption by spanish farmers facing the EU cotton sector reform

Cotton production in the European Union (EU) is limited to areas of Greece and Southern Spain (Andalusia). The 2004 reform of the EU cotton policy severely affected the profitability of the crop. In this article we analyze how the introduction of genetically modified (GM), insect-resistant cotton varieties (Bt cotton) might help EU cotton farmers to increase profitability and therefore face the cotton policy reform. We first study farmers’ attitudes toward adoption of Bt cotton varieties through a survey conducted in Andalusia (Southern Spain). The results show a positive attitude of Andalusian cotton farmers toward the Bt cotton varieties. Second, we perform an ex-ante analysis of the effects of introducing Bt cotton in Andalusia. Finally, we integrate the analysis of the effects of Bt cotton with the analysis of the EU cotton reform. Our results show that despite the significant economic benefits of Bt cotton, the current policy reform is likely to jeopardize the profitability of cotton production in the EU.

Bias from farmer self-selection in genetically modified crop productivity estimates: Evidence from Indian data

In the continuing debate over the impact of genetically modified (GM) crops on farmers of developing countries, it is important to accurately measure magnitudes such as farm-level yield gains from GM crop adoption. Yet most farm-level studies in the literature do not control for farmer self-selection, a potentially important source of bias in such estimates. We use farm-level panel data from Indian cotton farmers to investigate the yield effect of GM insect-resistant cotton. We explicitly take into account the fact that the choice of crop variety is an endogenous variable which might lead to bias from self-selection. A production function is estimated using a fixed-effects model to control for selection bias. Our results show that efficient farmers adopt Bacillus thuringiensis (Bt) cotton at a higher rate than their less efficient peers. This suggests that cross-sectional estimates of the yield effect of Bt cotton, which do not control for self-selection effects, are likely to be biased upwards. However, after controlling for selection bias, we still find that there is a significant positive yield effect from adoption of Bt cotton that more than offsets the additional cost of Bt seed.

Effects of a non-chemical nematicide combined with soil solarization for the control of root-knot nematodes

The effectiveness of a formulated bio-nematicide product containing lyophilized bacteria spores of Bacillus firmus was evaluated against root-knot nematodes (RKN) in greenhouse and field experiments. A decrease of second stage juveniles hatching from eggs was recorded by using the bio-nematicide at a dose of 0.9 g kg(-1) of soil while further a decrease was recorded by doubling the dose. However, the mortality rate decreased as the inoculurn level increased. Exposure of either second stage juveniles or egg masses to temperatures of 35-40 degrees C for 1-4 weeks had a marked effect on their survival. In a field experiment, the bio-nematicide was evaluated for its potential to control RKN either as a stand-alone method or in combination with soil solarization. The latter was tested for 15-30 days and the bionematicide was applied just before soil coverage with the plastic sheet or just after its removal. Soil solarization either for 15-30 days provided satisfactory control of RKN. The combination of soil solarization with the bio-nematicide improved nematode control and gave results similar to the chemical treatment. (c) 2007 Elsevier Ltd. All rights reserved.

Isolating the 'farmer' effect as a component of the advantage of growing genetically modified varieties in developing countries: a Bt cotton case study from Jalgaon, India

The present paper explores the 'farmer' effect in economic advantages often claimed for Bt cotton varieties (those with the endotoxin gene from Bacillus thuringiensis conferring resistance to some insect pests) compared to non-Bt varieties. Critics claim that much of the yield advantage of Bt cotton could be due to the fact that farmers adopting the technology are in a better position to provide inputs and management and so much of any claimed Bt advantage is an artefact rather than reflecting a real advantage of the variety per se. The present paper provides an in-depth analysis of 63 non-adopting and 94 adopting households of Bt cotton in Jalgaon, Maharashtra State, India, spanning the seasons 2002 and 2003. Results suggest that Bt adopters are indeed different from non-adopters in a number of ways. Adopters appear to specialize more on cotton (at least in terms of the land area they devote to the crop), spend more money on irrigation and grow well-performing non-Bt varieties of cotton (Bunny). Taking gross margin as the basis for comparison, Bt plots had 2.5 times the gross margin of non-Bt plots in both seasons. If only adopters are considered then the gross margin advantage of Bt plots reduces to 1.6 times that of non-Bt plots. This is still a significant advantage and could well explain the popularity of Bt in Maharashtra. However, it is clear that great care needs to be taken with such comparative studies.

Genetically modified insect resistance in cotton: some farm level economic impacts in India

The paper explores the impact of insect-resistant Bacillus thuringiensis (Bt) cotton on costs and returns over the first two seasons of its commercial release in three sub-regions of Maharashtra State, India. It is the first such research conducted in India based on farmers' own practices rather than trial plots. Data were collected for a total of 7793 cotton plots in 2002 and 1577 plots in 2003. Results suggest that while the cost of cotton seed was much higher for farmers growing Bt cotton relative to those growing non-Bt cotton, the costs of bollworm spray were much lower. While Bt plots had greater costs (seed plus insecticide) than non-Bt plots, the yields and revenue from Bt plots were much higher than those of non-Bt plots (some 39% and 63% higher in 2002 and 2003, respectively). Overall, the gross margins of Bt plots were some 43% (2002) and 73% (2003) higher than those of non-Bt plots, although there was some variation between the three sub-regions of the state. The results suggest that Bt cotton has provided substantial benefits for farmers in India over the 2 years, but there are questions as to whether these benefits are sustainable. (c) 2004 Elsevier Ltd. All rights reserved.

Inequality and GM crops: a case study of Bt cotton in India

Critics of genetically modified (GM) crops often contend that their introduction enhances the gap between rich and poor farmers, as the former group are in the best position to afford the expensive seed as well as provide other inputs such as fertilizer and irrigation. The research reported in this paper explores this issue with regard to Bt cotton (cotton with the endotoxtin gene from Bacillus thuringiensis conferring resistance to some insect pests) in Jalgaon, Maharashtra State, India, spanning the 2002 and 2003 seasons. Questionnaire–based survey results from 63 non–adopting and 94 adopting households of Bt cotton were analyzed, spanning 137 Bt cotton plots and 95 non–Bt cotton plots of both Bt adopters and non–adopters. For these households, cotton income accounted for 85 to 88% of total household income, and is thus of vital importance. Results suggest that in 2003 Bt adopting households have significantly more income from cotton than do non–adopting households (Rp 66,872 versus Rp 46,351) but inequality in cotton income, measured with the Gini coefficient (G), was greater amongst non–adopters than adopters. While Bt adopters had greater acreage of cotton in 2003 (9.92 acres versus 7.42 for non–adopters), the respective values of G were comparable. The main reason for the lessening of inequality amongst adopters would appear to be the consistency in the performance of Bt cotton along with the preferred non–Bt cultivar of Bt adopters—Bunny. Taking gross margin as the basis for comparison, Bt plots had 2.5 times the gross margin of non–Bt plots of non–adopters, while the advantage of Bt plots over non–Bt plots of adopters was 1.6 times. Measured in terms of the Gini coefficient of gross margin/acre it was apparent that inequality was lessened with the adoption of Bunny (G = 0.47) and Bt (G = 0.3) relative to all other non–Bt plots (G = 0.63). Hence the issue of equality needs to be seen both in terms of differences between adopters and non–adopters as well as within each of the groups.

Production risk, pesticide use and GM crop technology in South Africa

Technology involving genetic modification of crops has the potential to make a contribution to rural poverty reduction in many developing countries. Thus far, pesticide-producing Bacillus thuringensis (Bt) varieties of cotton have been the main GM crops under cultivation in developing nations. Several studies have evaluated the farm-level performance of Bt varieties in comparison to conventional ones by estimating production technology, and have mostly found Bt technology to be very successful in raising output and/or reducing pesticide input. However, the production risk properties of this technology have not been studied, although they are likely to be important to risk-averse smallholders. This study investigates the output risk aspects of Bt technology by estimating two 'flexible risk' production function models allowing technology to independently affect the mean and higher moments of output. The first is the popular Just-Pope model and the second is a more general 'damage control' flexible risk model. The models are applied to cross-sectional data on South African smallholders, some of whom used Bt varieties. The results show no evidence that a 'risk-reduction' claim can be made for Bt technology. Indeed, there is some evidence to support the notion that the technology increases output risk, implying that simple (expected) profit computations used in past evaluations may overstate true benefits.

Characterization of an escherichia coli elaC deletion mutant

The elaC gene of Escherichia coli encodes a binuclear zinc phosphodiesterase (ZiPD). ZiPD homologs from various species act as 3' tRNA processing endoribonucleases, and although the homologous gene in Bacillus subtilis is essential for viability [EMBO J. 22 (2003) 4534], the physiological function of E. coli ZiPD has remained enigmatic. In order to investigate the function of E. coli ZiPD we generated and characterized an E. coli elaC deletion mutant. Surprisingly, the E. coli elaC deletion mutant was viable and had wild-type like growth properties. Micro array-based transcriptional analysis indicated expression of the E. coli elaC gene at basal levels during aerobic growth. The elaC gene deletion had no effect on the expression of genes coding for RNases or amino-acyl tRNA synthetases or any other gene among a total of > 1300 genes probed. 2D-PAGE analysis showed that the elaC mutation, likewise, had no effect on the proteome. These results strengthen doubts about the involvement of E. coli ZiPD in tRNA maturation and suggest functional diversity within the ZiPD/ElaCl protein family. In addition to these unexpected features of the E. coli elaC deletion mutant, a sequence comparison of ZiPD (ElaCl) proteins revealed specific regions for either enterobacterial or mammalian ZiPD (ElaCl) proteins. (C) 2004 Elsevier Inc. All rights reserved.