Final report on research project PS2010, proof of concept of automated mapping of weeds in arable fields

Many weeds occur in patches but farmers frequently spray whole fields to control the weeds in these patches. Given a geo-referenced weed map, technology exists to confine spraying to these patches. Adoption of patch spraying by arable farmers has, however, been negligible partly due to the difficulty of constructing weed maps. Building on previous DEFRA and HGCA projects, this proposal aims to develop and evaluate a machine vision system to automate the weed mapping process. The project thereby addresses the principal technical stumbling block to widespread adoption of site specific weed management (SSWM). The accuracy of weed identification by machine vision based on a single field survey may be inadequate to create herbicide application maps. We therefore propose to test the hypothesis that sufficiently accurate weed maps can be constructed by integrating information from geo-referenced images captured automatically at different times of the year during normal field activities. Accuracy of identification will also be increased by utilising a priori knowledge of weeds present in fields. To prove this concept, images will be captured from arable fields on two farms and processed offline to identify and map the weeds, focussing especially on black-grass, wild oats, barren brome, couch grass and cleavers. As advocated by Lutman et al. (2002), the approach uncouples the weed mapping and treatment processes and builds on the observation that patches of these weeds are quite stable in arable fields. There are three main aspects to the project. 1) Machine vision hardware. Hardware component parts of the system are one or more cameras connected to a single board computer (Concurrent Solutions LLC) and interfaced with an accurate Global Positioning System (GPS) supplied by Patchwork Technology. The camera(s) will take separate measurements for each of the three primary colours of visible light (red, green and blue) in each pixel. The basic proof of concept can be achieved in principle using a single camera system, but in practice systems with more than one camera may need to be installed so that larger fractions of each field can be photographed. Hardware will be reviewed regularly during the project in response to feedback from other work packages and updated as required. 2) Image capture and weed identification software. The machine vision system will be attached to toolbars of farm machinery so that images can be collected during different field operations. Images will be captured at different ground speeds, in different directions and at different crop growth stages as well as in different crop backgrounds. Having captured geo-referenced images in the field, image analysis software will be developed to identify weed species by Murray State and Reading Universities with advice from The Arable Group. A wide range of pattern recognition and in particular Bayesian Networks will be used to advance the state of the art in machine vision-based weed identification and mapping. Weed identification algorithms used by others are inadequate for this project as we intend to collect and correlate images collected at different growth stages. Plants grown for this purpose by Herbiseed will be used in the first instance. In addition, our image capture and analysis system will include plant characteristics such as leaf shape, size, vein structure, colour and textural pattern, some of which are not detectable by other machine vision systems or are omitted by their algorithms. Using such a list of features observable using our machine vision system, we will determine those that can be used to distinguish weed species of interest. 3) Weed mapping. Geo-referenced maps of weeds in arable fields (Reading University and Syngenta) will be produced with advice from The Arable Group and Patchwork Technology. Natural infestations will be mapped in the fields but we will also introduce specimen plants in pots to facilitate more rigorous system evaluation and testing. Manual weed maps of the same fields will be generated by Reading University, Syngenta and Peter Lutman so that the accuracy of automated mapping can be assessed. The principal hypothesis and concept to be tested is that by combining maps from several surveys, a weed map with acceptable accuracy for endusers can be produced. If the concept is proved and can be commercialised, systems could be retrofitted at low cost onto existing farm machinery. The outputs of the weed mapping software would then link with the precision farming options already built into many commercial sprayers, allowing their use for targeted, site-specific herbicide applications. Immediate economic benefits would, therefore, arise directly from reducing herbicide costs. SSWM will also reduce the overall pesticide load on the crop and so may reduce pesticide residues in food and drinking water, and reduce adverse impacts of pesticides on non-target species and beneficials. Farmers may even choose to leave unsprayed some non-injurious, environmentally-beneficial, low density weed infestations. These benefits fit very well with the anticipated legislation emerging in the new EU Thematic Strategy for Pesticides which will encourage more targeted use of pesticides and greater uptake of Integrated Crop (Pest) Management approaches, and also with the requirements of the Water Framework Directive to reduce levels of pesticides in water bodies. The greater precision of weed management offered by SSWM is therefore a key element in preparing arable farming systems for the future, where policy makers and consumers want to minimise pesticide use and the carbon footprint of farming while maintaining food production and security. The mapping technology could also be used on organic farms to identify areas of fields needing mechanical weed control thereby reducing both carbon footprints and also damage to crops by, for example, spring tines. Objective i. To develop a prototype machine vision system for automated image capture during agricultural field operations; ii. To prove the concept that images captured by the machine vision system over a series of field operations can be processed to identify and geo-reference specific weeds in the field; iii. To generate weed maps from the geo-referenced, weed plants/patches identified in objective (ii).

Toxoplasma gondii antibodies in wild rodents and marsupials from the Atlantic Forest, state of São Paulo, Brazil

Toxoplasma gondii é um protozoário parasita que infecta animais de sangue quente, incluindo seres humanos. Pequenos roedores e marsupiais têm papel importante na epidemiologia do T. gondii, pois são fontes de infecção para os felídeos domésticos e selvagens. Amostras de soro de 151 roedores e 48 marsupiais, capturados na Mata Atlântica, Estado de São Paulo, Sudeste do Brasil, foram analisadas para a pesquisa de anticorpos anti-T. gondii. Os anticorpos foram detectados pelo Teste de Aglutinação Modificada (MAT ≥ 25), com 8,6% (13/151) dos roedores e 10,4% (5/48) dos marsupiais soropositivos, com títulos variando de 25 a 6.400 e de 25 a 3.200, respectivamente, para os roedores e os marsupiais. Três das oito espécies de roedores (Akodon spp., Oligoryzomys nigripes e Rattus norvegicus) e uma das quatro espécies de marsupiais (Didelphis aurita) apresentaram animais positivos. A presença de anticorpos anti-T. gondii foi descrita pela primeira vez no roedor Oligoryzomys nigripes.

DNA barcodes for Mexican Cactaceae, plants under pressure from wild collecting

DNA barcodes could be a useful tool for plant conservation. Of particular importance is the ability to identify unknown plant material, such as from customs seizures of illegally collected specimens. Mexican cacti are an example of a threatened group, under pressure because of wild collection for the xeriscaping trade and private collectors. Mexican cacti also provide a taxonomically and geographically coherent group with which to test DNA barcodes. Here, we sample the matK barcode for 528 species of Cactaceae including approximately 75% of Mexican species and test the utility of the matK region for species-level identification. We find that the matK DNA barcode can be used to identify uniquely 77% of species sampled, and 79-87% of species of particular conservation importance. However, this is far below the desired rate of 95% and there are significant issues for PCR amplification because of the variability of primer sites. Additionally, we test the nuclear ITS regions for the cactus subfamily Opuntioideae and for the genus Ariocarpus (subfamily Cactoideae). We observed higher rates of variation for ITS (86% unique for Opuntioideae sampled) but a much lower PCR success, encountering significant intra-individual polymorphism in Ariocarpus precluding the use of this marker in this taxon. We conclude that the matK region should provide useful information as a DNA barcode for Cactaceae if the problems with primers can be addressed, but matK alone is not sufficiently variable to achieve species-level identification. Additional complementary regions should be investigated as ITS is shown to be unsuitable

Abundance and diversity of wild bees along gradients of heavy metal pollution

1. Wild bees are one of the most important groups of pollinators in the temperate zone. Therefore, population declines have potentially negative impacts for both crop and wildflower pollination. Although heavy metal pollution is recognized to be a problem affecting large parts of the European Union, we currently lack insights into the effects of heavy metals on wild bees. 2. We investigated whether heavy metal pollution is a potential threat to wild bee communities by comparing (i) species number, (ii) diversity and (iii) abundance as well as (iv) natural mortality of emerging bees along two independent gradients of heavy metal pollution, one at Olkusz (OLK), Poland and the other at Avonmouth (AVO), UK. We used standardized nesting traps to measure species richness and abundance of wild bees, and we recorded the heavy metal concentration in pollen collected by the red mason bee Osmia rufa as a measure of pollution. 3. The concentration of cadmium, lead and zinc in pollen collected by bees ranged from a background level in unpolluted sites [OLK: 1·3, 43·4, 99·8 (mg kg−1); AVO: 0·8, 42·0, 56·0 (mg kg−1), respectively] to a high level on sites in the vicinity of the OLK and AVO smelters [OLK: 6·7, 277·0, 440·1 (mg kg−1); AVO: 9·3, 356·2, 592·4 (mg kg−1), respectively]. 4. We found that with increasing heavy metal concentration, there was a steady decrease in the number, diversity and abundance of solitary, wild bees. In the most polluted sites, traps were empty or contained single occupants, whereas in unpolluted sites, the nesting traps collected from 4 to 5 species represented by up to ten individuals. Moreover, the proportion of dead individuals of the solitary bee Megachile ligniseca increased along the heavy metal pollution gradient at OLK from 0·2 in uncontaminated sites to 0·5 in sites with a high concentration of pollution. 5. Synthesis and applications. Our findings highlight the negative relationship between heavy metal pollution and populations of wild bees and suggest that increasing wild bee richness in highly contaminated areas will require special conservation strategies. These may include creating suitable nesting sites and sowing a mixture of flowering plants as well as installing artificial nests with wild bee cocoons in polluted areas. Applying protection plans to wild pollinating bee communities in heavy metal-contaminated areas will contribute to integrated land rehabilitation to minimize the impact of pollution on the environment.

Climate change and the risks associated with delayed breeding in a tropical wild bird population

There is growing evidence of changes in the timing of important ecological events, such as flowering in plants and reproduction in animals, in response to climate change, with implications for population decline and biodiversity loss. Recent work has shown that the timing of breeding in wild birds is changing in response to climate change partly because individuals are remarkably flexible in their timing of breeding. Despite this work, our understanding of these processes in wild populations remains very limited and biased towards species from temperate regions. Here, we report the response to changing climate in a tropical wild bird population using a long-term dataset on a formerly critically endangered island endemic, the Mauritius kestrel. We show that the frequency of spring rainfall affects the timing of breeding, with birds breeding later in wetter springs. Delays in breeding have consequences in terms of reduced reproductive success as birds get exposed to risks associated with adverse climatic conditions later on in the breeding season, which reduce nesting success. These results, combined with the fact that frequency of spring rainfall has increased by about 60 per cent in our study area since 1962, imply that climate change is exposing birds to the stochastic risks of late reproduction by causing them to start breeding relatively late in the season.

Genetic diversity of red-fleshed apples (Malus)

Anthocyanins are flavonoid pigments imparting red, blue, or purple pigmentation to fruits, flowers and foliage. These compounds are powerful antioxidants in vitro, and are widely believed to contribute to human health. The fruit of the domestic apple (Malus x domestica) is a popular and important source of nutrients, and is considered one of the top ‘functional foods’—those foods that have inherent health-promoting benefits beyond basic nutritional value. The pigmentation of typical red apple fruits results from accumulation of anthocyanin in the skin. However, numerous genotypes of Malus are known that synthesize anthocyanin in additional fruit tissues including the core and cortex (flesh). Red-fleshed apple genotypes are an attractive starting point for development of novel varieties for consumption and nutraceutical use through traditional breeding and biotechnology. However, cultivar development is limited by lack of characterization of the diversity of genetic backgrounds showing this trait. We identified and cataloged red-fleshed apple genotypes from four Malus diversity collections representing over 3,000 accessions including domestic cultivars, wild species, and named hybrids. We found a striking range of flesh color intensity and pattern among accessions, including those carrying the MYB10 R 6 allele conferring ectopic expression of a key transcriptional regulator of anthocyanin biosynthesis. Although MYB10 R 6 was strongly associated with red-fleshed fruit among genotypes, this allele was neither sufficient nor required for this trait in all genotypes. Nearly all red-fleshed accessions tested could be traced back to ‘Niedzwetzkyana’, a presumed natural form of M. sieversii native to central Asia.

Supplementary feeding of wild birds indirectly affects the local abundance of arthropod prey

Providing supplementary food for wild birds is a globally popular past-time; almost half of the households in many developed countries participate and billions of US dollars are spent annually. Although the direct influence of this additional resource on bird survivorship and fecundity has been studied, there is little understanding of the wider ecological consequences of this massive perturbation to (what are usually) urban ecosystems. We investigated the possible effects of wild bird feeding on the size and survivorship of colonies of a widespread arthropod prey species of many small passerine birds, the pea aphid [Acyrthosiphon pisum (Harris); Hemiptera: Aphididae], in suburban gardens in a large town in southern England. We found significantly fewer aphids and shorter colony survival times in colonies exposed to avian predation compared to protected controls in gardens with a bird feeder but no such differences between exposed and protected colonies in gardens that did not feed birds. Our work therefore suggests that supplementary feeding of wild birds in gardens may indirectly influence population sizes and survivorship of their arthropod prey and highlights the need for further research into the potential effects on other species.

A double-decker bus, an elephant and 300 Girl Guides: analyzing 'space' and 'place' in Blue Peter

This article draws upon Karen Lury's definitions of 'space' and 'place' in relation to the BBC children's programme Blue Peter (1958–present). Through an analysis of the Blue Peter studio over the past 53 years, Amanda Beauchamp highlights its evolution from a 'space' to a 'place' within the history of children's television. Her article considers how the Blue Peter studio's 'infinite nature' was achieved, alongside the role it played in creating the programme institution. She addresses the impact of major changes in the studio layout since 2005, when the studio went from being 'tardis-like' to a 'cosy cubbyhole'. Amanda concludes by questioning the impact that this change has had on programme identity and whether the 'place' that pre-2005 Blue Peter took 47 years to create has been compromised.

Persistence of a wild type Escherichia coli and its multiple antibiotic-resistant (MAR) derivatives in the abattoir and on chilled pig carcasses

The aim of this study was to evaluate the ability of an Escherichia coli with the multiple antibiotic resistance (MAR) phenotype to withstand the stresses of slaughter compared to an isogenic progenitor strain. A wild type E. coli isolate (345-2RifC) of porcine origin was used to derive 3 isogenic MAR mutants. Escherichia coli 345-2RifC and its MAR derivatives were inoculated into separate groups of pigs. Once colonisation was established, the pigs were slaughtered and persistence of the E. coli strains in the abattoir environment and on the pig carcasses was monitored and compared. No significant difference (P>0.05) was detected between the shedding of the different E. coli strains from the live pigs. Both the parent strain and its MAR derivatives persisted in the abattoir environment, however the parent strain was recovered from 6 of the 13 locations sampled while the MAR derivatives were recovered from 11 of 13 and the number of MAR E. coil recovered was 10-fold higher than the parent strain at half of the locations. The parent strain was not recovered from any of the 6 chilled carcasses whereas the MAR derivatives were recovered from 3 out of 5 (P<0.001). This study demonstrates that the expression of MAR in 345-2RifC increased its ability to survive the stresses of the slaughter and chilling processes. Therefore in E. coli, MAR can give a selective advantage, compared to non-MAR strains, for persistence on chilled carcasses thereby facilitating transit of these strains through the food chain. (C) 2010 Elsevier B.V. All rights reserved.

Mutation in TERMINAL FLOWER1 reverses the photoperiodic requirement for flowering in the wild strawberry, Fragaria vesca

Photoperiodic flowering has been extensively studied in the annual short-day and long-day plants rice and Arabidopsis while less is known about the control of flowering in perennials. In the perennial wild strawberry, Fragaria vesca L. (Rosaceae), short-day and perpetual flowering long-day accessions occur. Genetic analyses showed that differences in their flowering responses are caused by a single gene, the SEASONAL FLOWERING LOCUS which may encode the F. vesca homolog of TERMINAL FLOWER1 (FvTFL1). We show through high-resolution mapping and transgenic approaches that FvTFL1 is the basis of this change in flowering behavior and demonstrate that FvTFL1 acts as a photoperiodically regulated repressor. In short-day F. vesca, long photoperiods activate FvTFL1 mRNA expression and short days suppress it, promoting flower induction. These seasonal cycles in FvTFL1 mRNA level confer seasonal cycling of vegetative and reproductive development. Mutations in FvTFL1 prevent LD suppression of flowering, and the early flowering that then occurs under LD is dependent on the F. vesca homolog of FLOWERING LOCUS T. This photoperiodic response mechanism differs from those described in model annual plants. We suggest that this mechanism controls flowering within the perennial growth cycle in F. vesca, and demonstrate that a change in a single gene reverses the photoperiodic requirements for flowering.

The short- and long-term fitness consequences of natal dispersal in a wild bird population

Dispersal is a key process in population and evolutionary ecology. Individual decisions are affected by fitness consequences of dispersal, but these are difficult to measure in wild populations. A long-term dataset on a geographically closed bird population, the Mauritius kestrel, offers a rare opportunity to explore fitness consequences. Females dispersed further when the availability of local breeding sites was limited, whereas male dispersal correlated with phenotypic traits. Female but not male fitness was lower when they dispersed longer distances compared to settling close to home. These results suggest a cost of dispersal in females. We found evidence of both short- and long-term fitness consequences of natal dispersal in females, including reduced fecundity in early life and more rapid aging in later life. Taken together, our results indicate that dispersal in early life might shape life history strategies in wild populations.

Pollinator community responses to the spatial population structure of wild plants: A pan-European approach

Land-use changes can alter the spatial population structure of plant species, which may in turn affect the attractiveness of flower aggregations to different groups of pollinators at different spatial scales. To assess how pollinators respond to spatial heterogeneity of plant distributions and whether honeybees affect visitation by other pollinators we used an extensive data set comprising ten plant species and their flower visitors from five European countries. In particular we tested the hypothesis that the composition of the flower visitor community in terms of visitation frequencies by different pollinator groups were affected by the spatial plant population structure, viz. area and density measures, at a within-population (‘patch’) and among-population (‘population’) scale. We found that patch area and population density were the spatial variables that best explained the variation in visitation frequencies within the pollinator community. Honeybees had higher visitation frequencies in larger patches, while bumblebees and hoverflies had higher visitation frequencies in sparser populations. Solitary bees had higher visitation frequencies in sparser populations and smaller patches. We also tested the hypothesis that honeybees affect the composition of the pollinator community by altering the visitation frequencies of other groups of pollinators. There was a positive relationship between visitation frequencies of honeybees and bumblebees, while the relationship with hoverflies and solitary bees varied (positive, negative and no relationship) depending on the plant species under study. The overall conclusion is that the spatial structure of plant populations affects different groups of pollinators in contrasting ways at both the local (‘patch’) and the larger (‘population’) scales and, that honeybees affect the flower visitation by other pollinator groups in various ways, depending on the plant species under study. These contrasting responses emphasize the need to investigate the entire pollinator community when the effects of landscape change on plant–pollinator interactions are studied.

Wild pollinators enhance fruit set of crops regardless of honey bee abundance

Diversity and abundance of wild-insect pollinators have declined in many agricultural landscapes. Whether such declines reduce crop yields, or are mitigated by managed pollinators such as honey bees, is unclear. Here, we show universally positive associations of fruit set with wild-insect visits to flowers in 41 crop systems worldwide, and thus clearly demonstrate their agricultural value. In contrast, fruit set increased significantly with visitation by honey bees in only 14% of the systems surveyed. Overall, wild insects pollinated crops more effectively, because increase in their visitation enhanced fruit set by twice as much as an equivalent increase in honey bee visitation. Further, visitation by wild insects and honey bees promoted fruit set independently, so high abundance of managed honey bees supplemented, rather than substituted for, pollination by wild insects. Our results suggest that new practices for integrated management of both honey bees and diverse wild-insect assemblages will enhance global crop yields.

Identifying key knowledge needs for evidence-based conservation of wild insect pollinators: a collaborative cross-sectoral exercise

In response to evidence of insect pollinator declines, organisations in many sectors, including the food and farming industry, are investing in pollinator conservation. They are keen to ensure that their efforts use the best available science. We convened a group of 32 ‘conservation practitioners’ with an active interest in pollinators and 16 insect pollinator scientists. The conservation practitioners include representatives from UK industry (including retail), environmental non-government organisations and nature conservation agencies. We collaboratively developed a long list of 246 knowledge needs relating to conservation of wild insect pollinators in the UK. We refined and selected the most important knowledge needs, through a three-stage process of voting and scoring, including discussions of each need at a workshop. We present the top 35 knowledge needs as scored by conservation practitioners or scientists. We find general agreement in priorities identified by these two groups. The priority knowledge needs will structure ongoing work to make science accessible to practitioners, and help to guide future science policy and funding. Understanding the economic benefits of crop pollination, basic pollinator ecology and impacts of pesticides on wild pollinators emerge strongly as priorities, as well as a need to monitor floral resources in the landscape.