In-Depth Observation on the Microbial and Fungal Community Structure of Four Contrasting Tomato Cultivation Systems in Soil Based and Soilless Culture Systems

As soil and soilless culture systems are highly dynamic environments, the structure of rhizosphere microbial communities is consistently adapting. There is a knowledge gap between the microbial community structure of soil based and soilless culture systems and thus we aimed at surveying their impact on diversity and composition of bacterial communities across a 10-month period in a tomato cultivation system. We compared community metrics between an soil based culture system fertilized with malt sprouts and blood meal, known for its slow and high mineralization rate, respectively and a soilless culture system fertilized with fish effluent or supplemented with an liquid organic fertilizer. Bacterial and fungal community composition was followed over time using two complementary techniques, phospholipid fatty acid analysis and 16S rRNA amplicon sequencing. Nitrogen dynamics and plant performance were assessed to provide insight on how bacterial diversity of soil and soilless microbial communities ultimately impacts productivity. Similar plant performance was observed in soilless culture systems and soil based system and yield was the highest with the aquaponics-derived fertilizer. Soil and soilless cultivating systems supplemented with different nitrogen-rich fertilizers differed on its characteristics throughout the experimental period. Fast-paced fluctuations in pH(H₂O) and nutrient cycling processes were observed in growing medium. Physicochemical characteristics changed over time and interacted with bacterial community metrics. Multivariate analysis showed that plant length, pH, Flavisolibacter, phosphorus, chloride, ammonium, potassium, calcium, magnesium, sodium, electrical conductivity, nitrate, sulfate, and the bacterial genera Desulfotomaculum, Solirubrobacter, Dehalococcoides, Bythopirellula, Steroidobacter, Litorilinea, Nonomuraea were the most significant factors discriminating between natural soils supplemented with animal and plant by-products. Long-term fertilizer regimes significantly changed the PLFA fingerprints in both the soilless culture and soil based culture system. The use of these by-products in the soil was positively associated with arbuscular mycorrhizal fungi (AMF), which may influence rhizosphere communities through root exudates and C translocation. Community structure was distinct and consistently different over time, despite the fertilizer supplementation. The fungal microbial community composition was less affected by pH, while the composition of the bacterial communities (Actinomycetes, Gram-negative bacteria, and Gram-positive bacteria) was closely defined by soil pH, demonstrating the significance of pH as driver of bacterial community composition. Fertilizer application may be responsible for variations over time in the ecosystem. Knowledge about the microbial interactions in tomato cultivating systems opens a window of opportunity for designing targeted fertilizers supporting sustainable crop production.

Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

Physiological basis of chilling tolerance and early-season growth in miscanthus

BACKGROUND AND AIMS

The high productivity of Miscanthus × giganteus has been at least partly ascribed to its high chilling tolerance compared with related C4 crops, allowing for a longer productive growing season in temperate climates. However, the chilling tolerance of M. × giganteus has been predominantly studied under controlled environmental conditions. The understanding of the underlying mechanisms contributing to chilling tolerance in the field and their variation in different miscanthus genotypes is largely unexplored.

METHODS

Five miscanthus genotypes with different sensitivities to chilling were grown in the field and scored for a comprehensive set of physiological traits throughout the spring season. Chlorophyll fluorescence was measured as an indication of photosynthesis, and leaf samples were analysed for biochemical traits related to photosynthetic activity (chlorophyll content and pyruvate, Pi dikinase activity), redox homeostasis (malondialdehyde, glutathione and ascorbate contents, and catalase activity) and water-soluble carbohydrate content.

KEY RESULTS

Chilling-tolerant genotypes were characterized by higher levels of malondialdehyde, raffinose and sucrose, and higher catalase activity, while the chilling-sensitive genotypes were characterized by higher concentrations of glucose and fructose, and higher pyruvate, Pi dikinase activity later in the growing season. On the early sampling dates, the biochemical responses of M. × giganteus were similar to those of the chilling-tolerant genotypes, but later in the season they became more similar to those of the chilling-sensitive genotypes.

CONCLUSIONS

The overall physiological response of chilling-tolerant genotypes was distinguishable from that of chilling-sensitive genotypes, while M. × giganteus was intermediate between the two. There appears to be a trade-off between high and efficient photosynthesis and chilling stress tolerance. Miscanthus × giganteus is able to overcome this trade-off and, while it is more similar to the chilling-sensitive genotypes in early spring, its photosynthetic capacity is similar to that of the chilling-tolerant genotypes later on.

Morpho-physiological responses to dehydration stress of perennial ryegrass and tall fescue genotypes

Worldwide drought stress is the most important restriction factor on food and fodder productivity. In this study, morpho-physiological adaptations to dehydration stress were investigated in two tall fescue (Festuca arundinacea Schreb.) genotypes (Fa13 and Fa19 with a high and low sheep grazing preference respectively) and Lolium perenne L. Drought stress as evaluated by decreasing stomatal conductance and chlorophyll content, chlorophyll fluorescence parameters and fructan concentration were first observed in L. perenne (16 days after the start of the drought stress). Furthermore, after 20 days of drought stress the activities of ascorbate peroxide (APX), catalase (CAT), and superoxide dismutase (SOD) were reduced in stressed plants indicating that the capacity to scavenge ROS diminished under severe stress though no differences between genotypes were observed. Osmotic adjustment by carbohydrates did also not differ between the genotypes. Proline, however, reached its highest level in drought-stressed L. perenne followed by Fa13 and Fa19 respectively. The studied species showed a similar degree in response in the traits assessed when plants were exposed to dehydration stress; however changes were first observed in L. perenne.

The effect of maize silage type on the performances and methane emission of dairy cattle

To examine whether type of maize silage is important for milk production performances, maize silage LG30224 (LG) was compared with Falkone (FA), the latter having a 4.0% points lower rumen NDF digestibility and 19 g/kg dry matter (DM) more starch. To bridge the lower energy content of FA, a third treatment was involved by adding maize meal (MM) in a ratio of 92/8 on DM (FA+MM). Maize and grass silage were fed ad libitum in a ratio of 65/35 on DM basis. Concentrates were supplemented individually to meet energy and protein requirements. The experiment was set up as a Latin square with three groups of nine Holstein cows during three periods of 3 weeks. In the last 2 weeks of each period, DM intake (DMI) and milk performances were measured. Each group included one cannulated cow to study effects on rumen fermentation. During the last 4 days of each period, two cows from each group were placed in gas exchange chambers to measure nutrient digestibility and methane production. Total DMI was higher (p < 0.05) for FA+MM (20.8 kg/day) than for FA (20.3 kg/day), while DMI for LG was intermediate (20.6 kg/day). Treatment did not affect milk production nor composition, whereas fat-protein-corrected milk was higher for LG (30.5 kg/day) and FA+MM (30.3 kg/day) than for FA (29.9 kg/day). The ration did not affect pH nor volatile fatty acid composition in the rumen. Further, total tract digestibility of OM, crude protein, NDF and starch did not differ among treatments. The ration with LG gave higher methane production per day and per kg NDF intake than both rations with FA, but the difference was not significant when expressed per kg DMI or FPCM. Thus, maize silage type is of little importance for milk production if energy and physical structure requirements are met.

Growing media constituents determine the microbial nitrogen conversions in organic growing media for horticulture

Vegetables and fruits are an important part of a healthy food diet, however, the eco‐sustainability of the production of these can still be significantly improved. European farmers and consumers spend an estimated €15.5 billion per year on inorganic fertilizers and the production of N‐fertilizers results in a high carbon footprint. We investigated if fertilizer type and medium constituents determine microbial nitrogen conversions in organic growing media and can be used as a next step towards a more sustainable horticulture. We demonstrated that growing media constituents showed differences in urea hydrolysis, ammonia and nitrite oxidation and in carbon dioxide respiration rate. Interestingly, mixing of the growing media constituents resulted in a stimulation of the function of the microorganisms. The use of organic fertilizer resulted in an increase in amoA gene copy number by factor 100 compared to inorganic fertilizers. Our results support our hypothesis that the activity of the functional microbial community with respect to nitrogen turnover in an organic growing medium can be improved by selecting and mixing the appropriate growing media components with each other. These findings contribute to the understanding of the functional microbial community in growing media and its potential role towards a more responsible horticulture.

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems

The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.

MOLECULAR INSIGHTS ON THE FUNCTIONAL MICROBIAL COMMUNITY FROM ORGANIC AND MINERAL GROWING MEDIA AND ITS INTERACTION WITH AGROBACTERIUM RHIZOGENES

Despite numerous preventative measures, the hairy roots syndrome is an increasing problem in greenhouse horticulture. A recent survey of 177 tomato, cucumber and eggplant growers in Flanders (Belgium) revealed an increase of this disease in the last two years, with about 26% of all the tomato crops showing the syndrome. In this study, we compared the physicochemical and microbial community characteristics of inorganic and organic growing media in relation to the presence of the causative agent of the hairy roots, the plant pathogen Agrobacterium rhizogenes. We aimed to identify how the microbial and environmental interactions influenced the development and spread of this disease in a soilless cultivation system. Multivariate statistical analysis performed to assess the characteristics of each growing media revealed key variables impacting the hosted microbial community. Thus, humidity, pH, potassium and conductivity were drivers of the differences among microbial community composition. High throughput sequencing analysis of the bacterial family abundance of the communities present in organic media indicated potential competitive interactions with A. rhizogenes. Based on our hypothesis that growing media hosted a particular microbiota with potential for modulating hairy roots, we determined how the environment in organic media is reshaped to avoid establishment of A. rhizogenes. Our methodology provides a comprehensive insight into the complex bacterial interactions in horticultural media, which may be potentially applied for the development of effective control strategies and decrease in economic losses.

HERBICIDE SENSITIVITY OF ECHINOCHLOA CRUS-GALLI POPULATIONS: A COMPARISON BETWEEN CROPPING SYSTEMS

Echinochloa crus-galli populations exhibit high morphological variability and their response to herbicides varies from field to field. Differential response to herbicides could reflect differences in selection pressure, caused by years of cropping system related herbicide usage. This study investigates the relation between herbicide sensitivity of Echinochloa crus-galli populations and the cropping system to which they were subjected. The herbicide sensitivity of Echinochloa crus-galli was evaluated for populations collected on 18 fields, representing three cropping systems, namely (1) a long-term organic cropping system, (2) a conventional cropping system with corn in crop rotation or (3) a conventional cropping system with long-term monoculture of corn. Each cropping system was represented by 6 E. crus-galli populations. All fields were located on sandy soils. Dose-response pot experiments were conducted in the greenhouse to assess the effectiveness of three foliar-applied corn herbicides: nicosulfuron (ALS-inhibitor), cycloxydim (ACCase-inhibitor) and topramezone (HPPD-inhibitor), and two soil-applied corn herbicides: S-metolachlor and dimethenamid-P (both VLCFA-inhibitors). Foliar-applied herbicides were tested at a quarter, half and full recommended doses. Soil-applied herbicides were tested within a dose range of 0-22.5 g a.i. ha(-1) for S-metolachlor and 0-45 g a.i. ha(-1) for dimethenamid-P. Foliar-applied herbicides were applied at the three true leaves stage. Soil-applied herbicides were treated immediately after sowing the radicle-emerged seeds. All experiments were performed twice. The foliage dry weight per pot was determined four weeks after treatment. Plant responses to herbicides were expressed as biomass reduction (%, relative to the untreated control). Sensitivity to foliar-applied herbicides varied among cropping systems. Compared to populations from monoculture corn fields, populations originating from organic fields were significantly more sensitive to cycloxydim, topramezone and nicosulfuron (resp. 5.3%, 5.9% and 12.3%). Populations from the conventional crop rotation system showed intermediate sensitivity levels. Contrary to foliar-applied herbicides, the effectiveness of soil-applied herbicides was not affected by cropping system. Integrated weed management may be necessary to preserve herbicide efficacy on the long term.

Seed germination, seedling emergence, seed persistence and triflusulfuron-methyl sensitivity in Galinsoga parviflora and G. quadriradiata

Galinsoga quadriradiota Ruiz and Pavon (hairy galinsoga) and Galinsogo parviflora Cav. (smaliflower galinsoga, gallant soldier) are very troublesome weeds in many vegetable row crops in Europe. In order to optimize further management strategies for Galinsoga control in-depth study of germination biology was performed. Germination experiments were conducted to evaluate the impact of light and alternating temperatures on germination of a large set of Galinsoga populations. Seedling emergence was investigated by burying seeds at different depths in a sand and sandy loam soil. Dormancy of fresh achenes harvested in autumn was evaluated by studying germination response in light at 25/20 degrees C with and without nitrate addition. Seed longevity was investigated in an accelerated ageing experiment by exposing seeds to 45 degrees C and 100% relative humidity. A dose-response pot experiment was conducted in the greenhouse to evaluate the effectiveness of triflusulfuron-methyl, applied at the one leaf pair stage, for controlling Belgian Galinsoga populations. Galinsoga seeds required light for germination; light dependency varied among populations. Seedling emergence decreased drastically with increasing burial depth. Maximum depth of emergence varied between 4 and 10mm depending on soil type and population. In a sandy soil, emergence percentages were higher and seedlings were able to emerge from greater depths than in a sandy loam soil. Freshly produced G. parviflora seeds showed a varying but high degree of primary dormancy and were less persistent than G. quadriradiata seeds which lack primary dormancy. Galinsoga parviflora populations were more sensitive to triflusulfuron-methyl than G. quadriradiata populations. The lack of primary dormancy, high seed persistence and lower herbicide sensitivity may explain the higher distribution and abundance of G. quadriradiata over G. parviflora populations in Belgium. Overall, features such as lack of primary dormancy of freshly harvested G. quadriradiata seeds and light dependency for germination may be used to optimize and develop Galinsoga management strategies.

Absorption, translocation and metabolism of metamitron in Chenopodium album

BACKGROUND

In recent years, common lambsquarters (Chenopodium album L.) populations from sugar beet fields in different European countries have responded as resistant to the as-triazinone metamitron. The populations have been found to have the same D1 point mutation as known for atrazine-resistant biotypes (Ser264 to Gly). However, pot experiments revealed that metamitron resistance is not as clear-cut as observed with triazine resistance in the past. The objectives of this study were to clarify the absorption, translocation and metabolic fate of metamitron in C. album.

RESULTS

Root absorption and foliar absorption experiments showed minor differences in absorption, translocation and metabolism of metamitron between the susceptible and resistant C. album populations. A rapid metabolism in the C. album populations was observed when metamitron was absorbed by the roots. The primary products of metamitron metabolism were identified as deamino-metamitron and metamitron-N-glucoside. PABA, known to inhibit the deamination of metribuzin, did not alter the metabolism of metamitron, and nor did the cytochrome P450 inhibitor PBO. However, inhibition of metamitron metabolism in the presence of the cytochrome P450 inhibitor ABT was demonstrated.

CONCLUSION

Metamitron metabolism in C. album may act as a basic tolerance mechanism, which can be important in circumstances favouring this degradation pathway.

Sensitivity of locally naturalized Panicum species to HPPD- and ALS-inhibiting herbicides in maize

Until recently the Panicum species Panicum schinzii Hack. (Transvaal millet), Panicum dichotomiflorum Michx. (Fall panicum) and Panicum capillare L. (Witchgrass) were completely overlooked in Belgium. Since 1970, these species have gradually spread and are now locally naturalized and abundant in and along maize fields. One of the possible raisons for their expansion in maize fields might be a lower sensitivity to postemergence herbicides acting against panicoid grasses, in particular those inhibiting 4-hydroxyphenyl pyruvate dioxygenase (HPPD) and acetolactate synthase (ALS). A dose-response pot experiment was conducted in the greenhouse to evaluate the effectiveness of five HPPD-inhibiting herbicides (sulcotrione, mesotrione, isoxaflutole, topramezone, tembotrione) and two ALS-inhibiting herbicides (nicosulfuron, foramsulfuron) for controlling Belgian populations of P. schinzii, P. dichotomiflorum and P. capillare. Shortly after sowing, half of all pots were covered with a film of activated charcoal to evaluate foliar activity of the applied herbicides. In another dose-response pot experiment, sensitivity of five local P. dichotomiflorum populations to HPPD-inhibitors and nicosulfuron was investigated. Finally, the influence of leaf stage at time of herbicide application on efficacy of topramezone and nicosulfuron for Panicum control was evaluated. Large interspecific differences in sensitivity to HPPD-inhibiting herbicides were observed. Panicum schinzii was sensitive (i.e., required a dose lower than the maximum authorized field dose to achieve 90% reduction in biomass) to tembotrione but moderately sensitive (i.e. required maximum field dose) to topramezone and poorly sensitive (i.e. required three-fold higher dose than maximum field dose) to mesotrione and sulcotrione. However, P. dichotomiflorum, a species that morphologically closely resembles P. schinzii, was sensitive to mesotrione and topramezone but moderately sensitive to tembotrione. All Panicum species were sensitive to low doses of nicosulfuron and foramsulfuron. The relative contribution from soil activity to weed control resulting from postemergence applications was important for isoxaflutole, sulcotrione, tembotrione and mesotrione but not for topramezone, nicosulfuron and foramsulfuron. Naturalized Panicum dichotomiflorum populations exhibited differential herbicide sensitivity profiles. Panicum schinzii, P. capillare and P.dichotomiflorum showed a progressive decrease in sensitivity to topramezone and nicosulfuron during seedling development. A satisfactory postemergence control of Panicum species in the field will require appropriate choice of herbicide and dose, as well as a more timely application (i.e. before weeds reach the four leaves stage).

The origin of metamitron resistant Chenopodium album populations in sugar beet

Chenopodium album L. is a major weed in spring-planted crops in the temperate regions of the world. Since 2000, farmers have reported an unsatisfactory control of this weed in sugar beet fields in Belgium, France and The Netherlands. Frequently, the surviving C. album plants are resistant to metamitron, a key herbicide in this crop. Metamitron resistance in C. album is caused by a Ser264 to Gly mutation in the psbA gene on the chloroplast genome, which prevents binding of metamitron to its target site. This mutation causes also resistance to other herbicides with a similar mode of action, like metribuzin -applied in potato- and atrazine in particular. Atrazine has been applied very frequently in maize in the 1970s and the 1980s, but is now banned in Europe due to environmental reasons. The persistent use of atrazine in maize confronted Belgian and other European farmers in the early 1980s with atrazine resistant C. album with the same Ser264 to Gly mutation. The problems with atrazine resistant C. album disappeared when other herbicides were applied in maize. Unfortunately, this is not the case for metamitron resistant C. album in sugar beet, because no replacement herbicide is readily available. The history of atrazine use in maize brought up a question concerning the origin of the current metamitron resistant C. album populations. Have these populations been selected locally by regular use of metamitron in sugar beet or did the selection occur earlier by atrazine use when maize was grown in the same fields? This would have serious implications regarding the reversibility of herbicide resistance. Therefore, soil samples were collected on 16 fields with different histories: five fields with an organic management over 25 years, two fields with a history of atrazine resistant C. album, five fields with metamitron resistant C. album in sugar beet and four fields which were under permanent grassland for 10 years, preceded by a regular rotation in which sugar beet was a key crop. The seeds of C. album were extracted from the soil and germinated on a germination table. Germinated seeds were allowed to grow in a growth chamber. Metamitron resistance was determined by a chlorophyll fluorescence test and leaf material was sampled for AFLP-analysis. For all fields, estimations were made of the size of the seed bank (i.e. an indirect estimate of population size), the frequency of resistant plants and the genetic diversity of resistant and susceptible populations. The results indicate that herbicide-resistant C. album populations are persistent and maintain their adaptive capacity, challenging future management of metamitron resistant C. album.

Sensitivity of Echinochloa muricata and Echinochloa crus-galli to HPPD- and ALS-inhibiting herbicides in corn

Until recently Echinochloa muricata var. microstachya Wiegand (rough barnyardgrass), an alien species native to North America, was completely overlooked in Belgium due to its close morphological resemblance to Echinochloa crus-galli (L.) P. Beauv. (barnyardgrass). E. muricata var. microstachya has gradually spread and is now locally naturalized and abundant in and along maize fields. One of the possible reasons for its expansion in maize fields, besides e.g. the lack of crop rotation, might be a lower sensitivity to postemergence herbicides acting against panicoid grasses, in particular 4-hydroxyphenyl pyruvate dioxygenase (HPPD)-inhibiting herbicides and acetolactate synthase (ALS) inhibiting herbicides. Dose-response pot experiments were conducted in the greenhouse to evaluate the effectiveness of four HPPD-inhibitor herbicides [topramezone (ARIETTA), mesotrione (CALLISTO), tembotrione (LAUDIS), sulcotrione (MIKADO) and the ALS-inhibitor herbicide nicosulfuron (KELVIN) for controlling local populations of E. crus-galli and E. muricata. Pots were planted with 25 seeds, thinned afterwards to 5 plants (one week after sowing) and irrigated by overhead sprinklers. Herbicides were applied at the 3-4 leaf stage (BBCH stage 13-14). Fresh biomass was harvested 28 d after treatment. In another dose-response pot experiment, the influence of leaf stage at time of herbicide application on efficacy of topramezone for (rough) barnyardgrass control was evaluated. Sensitivity to HPPD-inhibitor herbicides topramezone and sulcotrione was significantly lower for E. muricata populations than for E. crus-galli populations. However, nicosulfuron sensitivity of both species was similar. Compared to E. crus-galli, sensitivity of E. muricata to topramezone was more dependent on leaf stage. Due to the intragenus variability in sensitivity to HPPD-inhibitor herbicides, higher awareness is required for presence of E. muricata plants in maize fields in order to avoid insufficient "barnyardgrass" control.

Local spread of metamitron resistant Chenopodium album L. patches

Molecular markers can provide valuable information on the spread of resistant weed biotypes. In particular, tracing local spread of resistant weed patches will give details on the importance of seed migration with machinery, manure, wind or birds. This study investigated the local spread of metamitron resistant Chenopodium album L. patches in the southwest region of the province West-Flanders (Belgium). During the summer of 2009, leaf and seed samples were harvested in 27 patches, distributed over 10 sugar beet fields and 1 maize field. The fields were grouped in four local clusters. Each cluster corresponded with the farmer who cultivated these fields. A cleaved amplified polymorphic sequence (CAPS) procedure identified the Ser264 to Gly mutation in the D1 protein, endowing resistance to metamitron, a key herbicide applied in sugar beet. The majority of the sampled plants within a patch (97% on average) carried this mutation. Amplified fragment length polymorphism (AFLP) analysis was performed with 4 primer pairs and yielded 270 molecular markers, polymorphic for the whole dataset (303 samples). Analysis of molecular variance revealed that a significant part of the genetic variability was attributed to variation among the four farmer locations (12 %) and variation among Chenopodium album patches within the farmer locations (14%). In addition, Mantel tests revealed a positive correlation between genetic distances (linearised phipt between pairs of patches) and geographic distances (Mantel-coefficient significant at p = 0.002), suggesting isolation-by-distance. In one field, a decreased genetic diversity and strong genetic relationships between all the patches in this field supported the hypothesis of a recent introduction of resistant biotypes. Furthermore, genetic similarity between patches from different fields from the same farmer and from different farmers indicated that seed transport between neighbouring fields is likely to have an important impact on the spread of metamitron resistant biotypes.

Weed seed bank response to 12 years of different fertilization systems

Fertilizer amendments can impact weed populations in a variety of ways. This study evaluated the effects of 12 year-long applications of different fertilization systems on size and composition of the weed seed bank in a conventionally managed maize monoculture field. Fertilization systems included all factorial combinations of two dairy cattle slurry rates, three vegetable, fruit and garden waste (VFG) compost rates, and three synthetic N fertilizer rates. Soil samples were taken in each subplot in May 2008 after sowing and prior to herbicide application. Residues recovered from soil samples were tested for weed seedling emergence to characterize soil seed banks. Total weed seed bank density was affected by mineral N fertilization but not by compost or animal slurry application. Weed seed bank composition was related to compost amendment and mineral N fertilization. Annual compost amendments reduced seed bank density of some persistent species (e.g., Chenopodium album and Solanum nigrum) irrespective of mineral N fertilization. Compost is a promising tool for incorporation into integrated weed control strategies aimed at reducing weed seed bank persistence.

Genetic modification through oligonucleotide-mediated mutagenesis. A GMO regulatory challenge?

In the European Union, the definition of a GMO is technology-based. This means that a novel organism will be regulated under the GMO regulatory framework only if it has been developed with the use of defined techniques. This approach is now challenged with the emergence of new techniques. In this paper, we describe regulatory and safety issues associated with the use of oligonucleotide-mediated mutagenesis to develop novel organisms. We present scientific arguments for not having organisms developed through this technique fall within the scope of the EU regulation on GMOs. We conclude that any political decision on this issue should be taken on the basis of a broad reflection at EU level, while avoiding discrepancies at international level.

Quantifying the introgressive hybridisation propensity between transgenic oilseed rape and its wild/weedy relatives

In order to estimate the introgressive hybridisation propensity (IHP) between genetically modified (GM) oilseed rape (Brassica napus) and certain of its cross-compatible wild/weedy relatives at the landscape level, a conceptual approach was developed. A gene flow index was established enclosing the successive steps to successfully achieve introgressive hybridisation: wild/weedy relatives and oilseed rape should co-occur, have overlapping flowering periods, be compatible, produce viable and fertile progeny, and the transgenes should persist in natural/weedy populations. Each step was described and scored, resulting in an IHP value for each cross-compatible oilseed rape wild/weedy relative. The gene flow index revealed that Brassica rapa has the highest introgressive hybridisation propensity (IHP value = 11.5), followed by Hirschfeldia incana and Raphanus raphanistrum (IHP = 6.7), Brassica juncea (IHP = 5.1), Diplotaxis tenuifolia and Sinapis arvensis (IHP = 4.5) in Flanders. Based on the IHP values, monitoring priorities can be defined within the pool of cross-compatible wild/weedy oilseed rape relatives. Moreover, the developed approach enables to select areas where case-specific monitoring of GM oilseed rape could be done in order to detect potential adverse effects on cross-compatible wild/weedy relatives resulting from vertical gene flow. The implementation of the proposed oilseed rape-wild relative gene flow index revealed that the survey design of existing botanical survey networks does not suit general surveillance needs of GM crops in Belgium. The encountered hurdles to implement the gene flow index and proposals to acquire the missing data are discussed.

Short-term nematode population dynamics as influenced by the quality of exogenous organic matter

Abstract

The food specificity of nematodes, their high number of species and high abundance in every habitat where decomposition takes place, indicate that the structure of the nematode assemblage has a high information content. Since nematodes respond quickly to changes in soil management and since the nematode fauna can be efficiently analysed, the structure of the nematode assemblage offers an interesting instrument to assess changes in soil conditions. We studied the effect of five organic amendments on the short-term nematode population dynamics and compared them to minerally fertilised and unfertilised plots. The experiment was started in 2005, and samples were taken in spring and autumn 2006 and spring 2007. In spring 2006, no clear differences among treatments in the diversity of free-living nematodes were observed, probably since the organic amendments were applied only twice, of which the last application was carried out 7 months before the sampling. At the second and third sampling, the enrichment index in the organically amended plots was higher than in the unamended plots, owing to the organic matter application. However, in plots amended with farmyard manure and cattle slurry the number of bacterivores increased significantly, while in the compost plots the fungivorous nematodes tended to be higher. This resulted in a low channel index for the manure and slurry plots, indicating a predominant bacterial decomposition pathway, and a higher channel index in the compost plots, suggesting a greater proportion of fungal decomposition. These assumptions on the decomposition of the applied organic matter were strongly supported by the composition of the soil microbial community, determined through PLFA analysis: in the compost plots the bacteria to fungi ratio was lower than in the manure and slurry plots. At all sampling occasions there was a remarkably lower abundance of plant-parasitic nematodes in plots amended with slurry and manure, indicating a negative impact of both amendments on plant-parasitic nematodes. We can conclude from this study that the fertiliser regimes affected the nematode assemblage, but that more samplings in the future are certainly necessary to assess adequately the impact of the different organic amendments.

Environmental impact of herbicide regimes used with genetically modified herbicide-resistant maize

With the potential advent of genetically modified herbicide-resistant (GMHR) crops in the European Union, changes in patterns of herbicide use are predicted. Broad-spectrum, non-selective herbicides used with GMHR crops are expected to substitute for a set of currently used herbicides, which might alter the agro-environmental footprint from crop production. To test this hypothesis, the environmental impact of various herbicide regimes currently used with non-GMHR maize in Belgium was calculated and compared with that of possible herbicide regimes applied in GMHR maize. Impacts on human health and the environment were calculated through the pesticide occupational and environmental risk (POCER) indicator. Results showed that the environmental impact of herbicide regimes solely relying on the active ingredients glyphosate (GLY) or glufosinate-ammonium (GLU) is lower than that of herbicide regimes applied in non-GMHR maize. Due to the lower potential of GLY and GLU to contaminate ground water and their lower acute toxicity to aquatic organisms, the POCER exceedence factor values for the environment were reduced approximately by a sixth when GLY or GLU is used alone. However, the environmental impact of novel herbicide regimes tested may be underestimated due to the assumption that active ingredients used with GMHR maize would be used alone. Data retrieved from literature suggest that weed control efficacy is increased and resistance development delayed when GLY or GLU is used together with other herbicides in the GMHR system. Due to the partial instead of complete replacement of currently used herbicide regimes, the beneficial environmental impact of novel herbicide regimes might sometimes be reduced or counterbalanced. Despite the high weed control efficacy provided by the biotechnology-based weed management strategy, neither indirect harmful effects on farmland biodiversity through losses in food resources and shelter, nor shifts in weed communities have been demonstrated in GMHR maize yet. However, with the increasing adoption rate of GMHR maize and their associated novel herbicide regimes, this situation is expected to change in the short-term.

Diseases on wheat and triticale under the growing conditions of Lubumbashi (Congo RD)

The food production in Katanga is inadequate and causes food insecurity for more than 400.000 people. Nowadays the Katanga province relies for more than 75 % on imported wheat and wheat flour from neighbouring countries. The absence of adapted germplasm is one of the mean reasons for the low production levels of small grains and as consequence the disinteresting of farmers for producing wheat. To select well adapted genotypes a screening test with wheat (T. aestivum) and triticale (x Triticosecale Wittm.) was establish during the rainy season of 2006-2007 at the farm Kasapa (25 km outside Lubumbashi). Glume blotch (S. nodorum teleomorph: Leptosphaeria nodorum) was the most dominant disease during the rainy season 2006 - 2007. Glume blotch could be detected on leaves and ears of wheat as well as of triticale. Fusarium head blight (Fusarium sp. teleomorph: Gibberella sp.) was also present but to a less extend. Rust or mildew fungus were not recorded on any genotype. The disease pressure made it possible to screen more disease tolerant genotypes of wheat and triticale. The differences were most clear for ear glume blotch but especially on triticale differences between FHB tolerant and susceptible genotypes could be made. For triticale and wheat respectively 25 and 32 % of the genotypes were put in the breeding pole to select new varieties.

The interplay between societal concerns and the regulatory frame on GM crops in the European Union

Recapitulating how genetic modification technology and its agro-food products aroused strong societal opposition in the European Union, this paper demonstrates how this opposition contributed to shape the European regulatory frame on GM crops. More specifically, it describes how this opposition contributed to a de facto moratorium on the commercialization of new GM crop events in the end of the nineties. From this period onwards, the regulatory frame has been continuously revised in order to slow down further erosion of public and market confidence. Various scientific and technical reforms were made to meet societal concerns relating to the safety of GM crops. In this context, the precautionary principle, environmental post-market monitoring and traceability were adopted as ways to cope with scientific uncertainties. Labeling, traceability, co-existence and public information were installed in an attempt to meet the general public request for more information about GM agro-food products, and the specific demand to respect the consumers' and farmers' freedom of choice. Despite these efforts, today, the explicit role of public participation and/or ethical consultation during authorization procedures is at best minimal. Moreover, no legal room was created to progress to an integral sustainability evaluation during market procedures. It remains to be seen whether the recent policy shift towards greater transparency about value judgments, plural viewpoints and scientific uncertainties will be one step forward in integrating ethical concerns more explicitly in risk analysis. As such, the regulatory frame stands open for further interpretation, reflecting in various degrees a continued interplay with societal concerns relating to GM agro-food products. In this regard, both societal concerns and diversely interpreted regulatory criteria can be inferred as signaling a request - and even a quest - to render more explicit the broader-than-scientific dimension of the actual risk analysis.

The co-existence between transgenic and non-transgenic maize in the European Union: a focus on pollen flow and cross-fertilization

The ongoing discussion on the co-existence between genetically modified (GM) and non-GM crops becomes more important in the European Union (EU). With the recent inscription of 17 GM maize varieties in the common EU catalogue of varieties of agricultural plant species, the acreage of transgenic maize for market purposes is expected to increase in some European countries. In the EU, specific tolerance thresholds have been established for the adventitious and technically unavoidable presence of GM material in non-GM produce, and member states are elaborating legal frames to cope with co-existence. As maize is a cross-pollinated crop relying on wind for the dispersal of its pollen, technical management measures will be imposed to reduce cross-fertilization between transgenic and non-transgenic maize. Various biological, physical and analytical parameters have been identified to play a role in the study of cross-fertilization in maize. This variability may hamper the comparison between research results and may complicate the definition of appropriate isolation distances and/or pollen barriers in order to limit out-crossing. The present review addresses these parameters and proposes containment measures in order to not exceed the legal labeling thresholds in maize.

Impact of field margin vegetation and herbage removal on ingrowing and anemochorous weeds

This research studies the effect of different ways to establish and to maintain unfertilised field margins on the development of potential weed plants and seed dispersal into adjacent crops. Plant communities in field margins either developed spontaneously or were sown with different seed mixtures of grasses and forbs. Margins were mown twice a year and the cuttings were either removed or not. Three years after establishment, the importance of important weeds Elymus repens, Cirsium arvense and Urtica dioica was significantly higher in the unsown community or when cuttings were not removed after mowing. Seed dispersal from the margin into adjacent crops was important in the unsown community during the first year after establishment. Between 82% and 99% of the seeds were disseminated within a distance of 4 m from the margin strip. In order to minimize the dissemination of weed species and invasion by noxious vegetatively propagated weeds it is recommended to establish a field margin by sowing and to remove the cuttings after each mowing cut.

Management of herbicide-tolerant oilseed rape in Europe: a case study on minimizing vertical gene flow

The potential commercialization of genetically modified herbicide-tolerant (GMHT) oilseed rape in Europe raises various concerns about their potential environmental and agronomic impacts, especially those associated with the escape of transgenes. Pollen of oilseed rape can be dispersed in space, resulting in the fertilization of sympatric compatible wild relatives (e.g. Brassica rapa) and oilseed rape cultivars grown nearby (GM and/or non-GM Brassica napus). The spatial and temporal dispersal of seeds of oilseed rape may lead to feral oilseed rape populations outside the cropped areas and oilseed rape volunteers in subsequent crops in the rotation. The incorporation of a HT trait(s) may increase the fitness of the recipient plants, making them more abundant and persistent, and may result in weeds that are difficult to control by the herbicide(s) to which they are tolerant. Vertical gene flow from transgenic oilseed rape to non-GM counterparts may also have an impact on farming and supply chain management, depending on labelling thresholds for the adventitious presence of GM material in non-GM products. Given the extent of pollen and seed dispersal in oilseed rape, it is obvious that the safe and sound integration of GMHT oilseed rape in Europe may require significant on-farm and off-farm management efforts. Crucial practical measures that can reduce vertical gene flow include (1) isolating seed production of Brassica napus, (2) the use of certified seed, (3) isolating fields of GM oilseed rape, (4) harvesting at the correct crop development stage with properly adjusted combine settings, (5) ensuring maximum germination of shed seeds after harvest, (6) controlling volunteers in subsequent crops, and (7) keeping on-farm records. The implementation of the recommended practices may, however, be difficult, entailing various challenges.

Biodiversity and agro-ecology in field margins

This multidisciplinary study investigates agro-ecological functions (nature conservation, agriculture, environment) and implications of newly created, mown sown and unsown field margin strips installed on ex-arable land to increase biodiversity. From conservational concern, the development of species rich field margin strips was not strongly affected by the installed type of margin strip since species diversity converged over time, whether strips were sown or not. Convergence between unsown and sown margin strips occurred also in terms of species composition: unsown and sown strips became similar over time. Mowing without removal of cuttings significantly reduced species richness, yielded more grassy margin strips and delayed similarity in species composition between sown and unsown margin strips. Species richness on the longer term was not significantly affected by light regime nor by disturbance despite significant temporary effects shortly after the disturbance event. On the contrary vegetation composition in terms of importance of functional groups changed after disturbance: the share of spontaneous species within functional groups increased resulting in higher similarity between the sown and unsown vegetation. Furthermore risk of invasion was highest in the disturbed unsown community on the unshaded side of a tree lane. A positive effect of botanical diversity on insect number and diversity was found. However the effects of botanical diversity on insect number was mediated by light regime. At high light availability differences between plant communities were more pronounced compared to low light availablilty. The abundance of some insect families was dependent on the vegetation composition. Furthermore light availability significantly influenced insect diversity as well as the spatial distribution of families. From agricultural concern, installing margin strips by sowing a species mixture and a mowing regime with removal of cuttings are good practices to diminish the risk of species ingrowth into adjacent crops by creeping roots and rhizomes. Seed dispersal was only problematic one year after the installation of the field margin strips particularly nearby the unsown margin strip and wind-borne seeds were dispersed over limited distances, mainly within 4 m of field margins. Annual herbage yield was not affected by mowing management. DM yield of sown/unsown communities converged over time. Compared to herbage from an intensively managed fertilized grassland, field margin herbage revealed a low feeding value, owing to a low crude protein content, a low digestibility and a high crude fibre content. The unsown community had a higher forage quality than communities sown to bred commercially available grass varieties. Both digestibility and crude protein content decreased over time irrespective of plant community or location. Mid June cuts were more productive than mid September cuts but digestibility and crude protein content was lower. The use of herbage from field margins as hay for horses or as a component in farmland compost are good alternatives. A strong relation was found between the distribution of pest insects and their antagonist families along field margin strips indicating a status of biological equilibrium. From environmental concern, field margin strips buffered boundary vegetation and watercourses against cropped areas loaded with high levels of mineral nitrogen. Margin strips reduced the mineral nitrogen content of the soil in the margin and mineral nitrogen loss during wintermonths. Mineral nitrogen loss was not affected by field margin type but by distance from the field crop. A minimal width of 5 m is necessary to reach an optimal reduction in mineral soil N and N losses.

The quantitative and qualitative difference between a F1 hybrid of maize and its F2 generation

The majority of modern maize varieties are single F1 hybrids. The yield performance of the F2 generation is known to be inferior to the F1 yield performance. We crossed several F1 hybrids and compared these crossings, together with true F2 generations, with the original F1s. Compared to the F1 generation, biomass yield in the F2 generation dropped with -26.7%, and with -8.7% in the crossings. Ear yield dropped with -35.3% and -10.7% respectively. F2 generations had a reduced early vigour and the ear filling startedlater. The yield of some F1 diallel crosses was not significantly different from the yield of the parental F1s.

Vegetation development and floristical diversity of newly created sown and unsown field margin strips on ex arable land during the first 3 successional years

Early succesion of newly created sown/unsown margin strips on ex arableland, managed by two cuttings per year with/without removal of cuttings was characterised by the replacement of annuals in favour of perennials, a steadily increase in the importance of monocots and a decrease in non N-fixing dicots. Mowing with removal of cuttings delayed this succession pattern. Sorenson's qualitative similarity index (based solely on species occurrence) revealed that species composition of the sown communities (in terms of species occurrence) became increasingly similar to the unsown plots. Furthermore convergence in vegetation composition between sown and unsown plots occurred also in terms of species importance as assessed by Sorenson's quantitative index (based on the combination of species occurrence and importance). Similarity in species importance (but not of species occurrence) was significantly enhanced by cutting with removal of cuttings. During the first 3 successional years, species diversity of sown and unsown communities converged in time, irrespective of mowing regime or location. The decrease in species diversity, number of sown wildflower species and wildflower density of sown communities was more pronounced under a mowing regime without removal of cuttings. The annual addition of mown roadside herbage significantly enhanced species richness but not the importance of dicots.

Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils

Agricultural practices, such as mineral nitrogen fertilization, have an impact on the soil's ability to oxidize methane, but little is known about the shifts in the methanotrophic community composition associated with these practices. Therefore, the long-term effect of both mineral (NH4NO3) and organic (manure and GFT-compost) fertilizer applications on the soil methanotrophic community activity and structure were investigated. Both high and low affinity methane oxidation rates were lower in the soil treated with mineral fertilizer compared to the other soils. An enhanced nitrate concentration was observed in the mineral fertilized soil but nitrate did not show a direct affect on the high affinity methane oxidation. In contrast, the low affinity methane oxidation was slowed down by increased nitrate concentrations, which suggests a direct effect of nitrate on low affinity methane oxidation. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments specific for methanotrophs revealed a distinct community between the mineral and organic fertilized soils as extra Type I methanotrophic bands (phylotypes) became visible in the organic fertilized soils. These phylotypes were not visible in the patterns of the added organic fertilizers suggesting an indirect effect of the organic fertilizers on the methanotrophic community. Additionally, a molecular analysis was performed after the low affinity methane oxidation test. The enhanced methane concentrations used in the test enriched certain low affinity methanotrophs in the organic fertilized soils but not in the mineral fertilized soil. Supporting the molecular and functional observations, fatty acids characteristic for methanotrophs were less abundant in the soil treated with mineral fertilizer compared to the soil treated with compost. In conclusion, the function and molecular and chemical composition of the methanotrophic community are all altered in soil fertilized with mineral fertilizer.

Disentangling invasiveness and invasibility during invasion in synthesized grassland communities

•   An experiment with synthesized grassland communities was performed to identify plant traits that contribute to invasiveness and community traits that promote invasibility, and to study the relationship between, and the relative importance of, invasiveness and invasibility. •   Eight perennial grass species were used both as invasible monocultures and as potential invaders in gaps in these monocultures. Invasion success in the establishment phase, and invader and monoculture traits were assessed. •   Invasion success expressed as germination correlated significantly with germination time (invader trait), light penetration in the gaps and N acquisition by the edge plants (monoculture traits). Success expressed as leaf length correlated with seed mass, germination time (invader traits) and light penetration. Forty-six per cent of the variation in germination was explained by invader identity and 8% by monoculture identity, whereas, for leaf length, they explained 15% and 18%, respectively. •   Regenerative traits (seed mass and germination time) correlated with invasiveness, and resource availability (light and nitrogen) with invasibility. The results suggest that species characteristics would largely determine the extent of an invasion event (number of seedlings), while the success of individual invaders (growth and survival) is determined by both species and ecosystem characteristics.

Molecular markers for cold tolerance and early vigour in maize (Zea mays L.)

Planting maize earlier than the current guidelines recommend, would give great contributions to ecological and sustainable agriculture. In order to plant maize earlier, maize varieties with good cold tolerance and strong early vigour are required. Therefore cold tolerance and early vigour should be important goals in modern maize breeding programmes. Both traits however have a complex, quantitative genetic background and are therefore not easily introduced into modern maize varieties. Marker assisted selection (MAS) can improve the efficiency of breeding activities. In this research project we aim to identify the molecular markers for cold tolerance and early vigour in one of our breeding populations through a QTL analysis. So far nine QTLs for cold tolerance and six QTLs for early vigour could be identified and there is even one QTL in common for the two traits under investigation. The analysis of more populations should reveal whether or not these QTLs might be useful in maize breeding programmes over the world.

Agricultural effects on yield and nutritive value of grassland under a limited fertilisation rate on sandy soils in Flanders

From 1999 to 2002, we studied the yield production and quality parameters of grassland installed on sandy soils (1) under normal management (NM), (2) under management with respect to meadow birds (MBM) -first mowing date 15 June or later- and (3) under botanical management (BM) -first mowing date 1 July or later. The experiments were conducted at two locations, Aalter and Geel. The biomass production under MBM and BM decreased by resp. 19% and 46% as compared to the NM. The nitrogen content in the vegetation of the delayed first cut (without fertilisation) of MBM (2.4%) and BM (2.3%) was much lower than under NM (3.3%). Since the first cut makes the major part of the total annual dry matter yield (43% for MBM and 59% for BM), the average nitrogen content of the overall DM yield dropped substantially if the first cut was delayed. The same phenomenon occurred for the digestibility of the organic matter: overall 66% for MBM and 59% for BM as compared to 69% for NM. The digestibility was partially influenced by the botanical composition. MBM resulted in a shift in botanical composition, favouring Poa trivialis L., Ranunculus repens L., and Holcus lanatus L. as compared to NM. BM mainly favoured Holcus lanatus L., and Ranunculus repens L. as compared to NM. Under the management types with delayed first cut, problems with residual mineral soil N never occurred.

Do conventionally and biologically cultivated soils differ in bacterial diversity and community structure?

The effects of a long-term herbicide treatment on the microbial community of an agricultural soil were investigated. Therefor, molecular techniques were used to evaluate the structure and diversity of the soil microbial community. Eubacterial and group-specific primers for methanotrophs type I and II were used to amplify 16S rRNA gene fragments from total soil DNA. These fragments were subsequently separated by denaturing gradient gel electrophoresis (DGGE). The structure of the methanotrophic community was affected by the herbicides as the patterns obtained from a herbicide treated soil (conventional) clustered separately from the control soil (biological). It seems that group-specific PCR followed by DGGE is a very powerful and sensitive technique to differentiate fields, which have received a herbicide treatment from those who did not. The diversity of the methanotrophic community was quantified by calculating the Shannon-Weaver index of biodiversity. The type I methanotrophs showed a significant decreased biodiversity due to the herbicide treatment but the diversity of the methanotrophs type II was slightly higher in the herbicide treated soil.

Seed vigour in Iranian wheat seeds exposed to cold condition

Cold stress occurring in the seedbed of winter wheat at the end of autumn results in reduced emergence, even of undeteriorated seed lots (which have not been subjected to a long period of storage and have not been kept in bad storage conditions). The purpose of the present study was to determine the ability of different wheat cultivars at emerging at low field temperatures and the usefulness of a number of laboratory tests in predicting relative emergence of undeteriorated seed lots of different wheat cultivars. Due to genotype variability there were different categories of vigour tested through field and laboratory tests. There were no significant correlations between laboratory tests and field emergence. Our results suggest that conventional vigour tests like standard germination and accelerated ageing do not have enough capacity for identifying genotype differences when emerging in cold conditions.