Managing biodiversity for ecosystem services in apple orchards

Conventional intensive agriculture is largely reliant on high agrochemical inputs and has resulted in damaging environmental impacts including large scale biodiversity loss. More environmentally sustainable agricultural production methods are required. Ecological intensification is an approach which aims to sustainably increase production by using biodiversity-derived ecosystem services and replacing agrochemical inputs where possible. This can be achieved through modifying agricultural management practices to support ecosystem service-providing beneficial species. This thesis investigates the ecological intensification of commercial apple orchards in the UK. Apples are one of the most economically and nutritionally important fruit crops globally and their production relies upon a number of ecosystem services including pollination, pest regulation, and soil fertility services. Alleyway cover crops were trialled as a novel management practice which has the potential to improve a number of orchard ecosystem services. Three different cover crop species mixtures, all based on perennial legumes but each with a different rationale, were compared to a standard mown-grass control. Growing cover crops in the alleyways was provided improved habitat quality for beneficial species, attracting greater numbers of natural enemy taxa including predatory beetles, parasitoids, and active-hunting spiders, without increasing the abundance of crop pests. Greater numbers of pollinators were also observed in alleyways sown with cover crops. Despite the greater numbers of beneficial species recorded in the cover crop treatments, no increases in pest regulation or pollination services were detected and no change in production was observed during the timescale of the study. A second potential benefit of alleyway cover crops is the production of mulch material. Traditionally, organic mulches were used in orchards to help supress weeds underneath the trees, increase soil nutrients, and retain soil moisture, however many of these functions have now been replaced by agrochemical inputs. The cuttings from alleyway cover crops can provide an in-situ source of mulching material. Alleyway cuttings were compared to two traditional mulch materials, compost and straw, and a standard no-mulch control. Alleyway cover crop cuttings boosted numbers of earthworms and enhanced leaf litter decomposition, whilst the traditional straw and compost mulches improved some soil fertility measures including soil organic matter and moisture when compared to the control. In the final study of the thesis, the importance of pollination is quantified and the methods used to assess pollinator dependence and pollination deficits are tested, with recommendations made about the scale at which these experiments should be carried out. Following pollinator exclusion apple yields were found to fall to 55% whilst supplementary hand pollination led yields to increase to 167% of current ‘open’ pollination rates, showing that pollination deficits existed in the study orchards. This study also highlights the importance of pollination for fruit quality, a key deciding factor of a crop’s economic value. Alleyway cover cropping was found to have positive effects on ecosystem service providers both above and below ground. Even relatively inexpensive cover crop mixtures, combined with a reduction in mowing frequency and increase in mowing height, were found to increase numbers of beneficial species. The findings demonstrate the potential benefits of this multi-purpose habitat management method

Traditional and cover crop-derived mulches enhance soil ecosystem services in apple orchards

Organic mulches are a traditional method of groundcover management in temperate commercial orchards, now largely replaced by herbicides and synthetic fertilisers. As a potential contribution to improving orchard sustainability, we hypothesised that the addition of organic mulches would: (H1) improve soil fertility and lead to greater tree growth and yields; (H2) support a larger and more biologically active community of soil organisms, assessed as increased soil respiration and greater earthworm numbers and biomass; and (H3) increase leaf litter decomposition and burial, potentially reducing the risk of apple scab disease (Venturia inaequalis). Cuttings from two legume-based cover crop mixtures grown in the alleyway spaces between tree rows and two traditional mulch materials, straw and compost, were trialled alongside a bare soil business-as-usual control for two years, using a randomized complete block design in a conventionally managed commercial ‘Gala’ apple orchard in the UK. Compared to the control, the compost mulch significantly increased both soil carbon and nitrogen by over 50 %. The straw mulch effectively suppressed weeds by about 90 % and increased soil moisture by about 5 %. Cover crop cuttings increased moisture levels and increased earthworm numbers and mass by 1.7 and 1.8 times greater respectively in the double-rate ‘legume-grass’ cuttings treatment. Increasing the quantity of cover crop cuttings produced more positive effects; the cumulative addition of cuttings can benefit several soil-derived ecosystem services. This study took place in a commercial apple orchard, the findings may therefore be applicable to other orchard and row-grown perennial crops

Coupled versus uncoupled hindcast simulations of the Madden-Julian oscillation in the Year of Tropical Convection

This study investigates the impact of a full interactive ocean on daily initialised 15 day hindcasts of the Madden-Julian oscillation (MJO), measured against a Met Office Unified Model (MetUM) atmosphere control simulation (AGCM) during a 3 month period of the Year of Tropical Convection (YOTC). Results indicated that the coupled configuration (CGCM) extends MJO predictability over that of the AGCM, by up to 3-5 days. Propagation is improved in the CGCM, which we partly attribute to a more realistic phase relationship between sea surface temperature (SST) and convection. In addition, the CGCM demonstrates skill in representing downwelling oceanic Kelvin and Rossby waves which warm SSTs along their trajectory, with the potential to feed back on the atmosphere. These results imply that an ocean model capable of simulating internal ocean waves may be required to capture the full effect of air-sea coupling for the MJO

Metamorphism of the Sierra de Maz and implications for the tectonic evolution of the MARA terrane

The Mesoproterozoic MARA terrane of western South America is a composite igneous-metamorphic complex that is important for Paleozoic paleogeographic reconstructions and the relative positions of Laurentia and Gondwana. The magmatic and detrital records of the MARA terrane are consistent with a Laurentian origin; however, the metamorphic and deformation records lack sufficient detail to constrain the correlation of units within the MARA terrane and the timing and mechanisms of accretion to the Gondwana margin. Combined regional mapping, metamorphic petrology, and garnet and monazite geochronology from the Sierra de Maz of northwest Argentina suggest that the region preserves four distinct litho-tectonic units of varying age and metamorphic conditions that are separated by middle- to lower-crustal ductile shear zones. The Zaino and Maz Complexes preserve Barrovian metamorphism and ages that are distinct from other units within the region. The Zaino and Maz Complexes both record metamorphism ca. 430–410 Ma and show no evidence of the regional Famatinian orogeny (ca. 490–455 Ma). In addition, the Maz Complex records an earlier granulite facies event at ca. 1.2 Ga. The Taco and Ramaditas Complexes, in contrast, experienced medium- and low-pressure upper amphibolite to granulite facies metamorphism, respectively, between ca. 470–460 Ma and were later deformed at ca. 440–420 Ma. The Maz shear zone that bounds the Zaino and Maz Complexes records sinistral oblique to sinistral deformation between ca. 430–410 Ma. The data suggest that at least some units in the MARA terrane were accreted by translation, and the Gondwana margin of northwest Argentina transitioned from a dominantly convergent margin to a highly oblique margin in the Silurian

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (λ) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty (“Forward” scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores (“Viterbi” scores) are Gumbel-distributed with constant λ = log 2, and the high scoring tail of Forward scores is exponential with the same constant λ. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments

Neutrophil Responses to Sterile Implant Materials

In vivo implantation of sterile materials and devices results in a foreign body immune response leading to fibrosis of implanted material. Neutrophils, one of the first immune cells to be recruited to implantation sites, have been suggested to contribute to the establishment of the inflammatory microenvironment that initiates the fibrotic response. However, the precise numbers and roles of neutrophils in response to implanted devices remains unclear. Using a mouse model of peritoneal microcapsule implantation, we show 30–500 fold increased neutrophil presence in the peritoneal exudates in response to implants. We demonstrate that these neutrophils secrete increased amounts of a variety of inflammatory cytokines and chemokines. Further, we observe that they participate in the foreign body response through the formation of neutrophil extracellular traps (NETs) on implant surfaces. Our results provide new insight into neutrophil function during a foreign body response to peritoneal implants which has implications for the development of biologically compatible medical devices

Quantifying crop pollinator-dependence and pollination deficits: the effects of experimental scale on yield and quality assessments

Many crops are known to be dependent on biotic pollination, but knowledge gaps remain regarding the extent of this dependence, how it varies between crop varieties, and the implications of biotic pollination for crop quality. Data is also lacking on the prevalence and extent of pollination deficits and the ability of the surrounding pollinator community to provide pollination services. Robust and standardised methodologies are crucial for pollination studies. However, there has been only limited research into the critical question of the appropriate scale to apply these methods. Here, we use a commercially important UK apple Malus domestica variety (Gala) to address the questions of pollinator-dependence and pollination deficits, quality benefits arising from pollination, and the implications of conducting pollination experiments at three different scales: the inflorescence, the branch, and the whole plant. We found that Gala apple production was highly dependent on biotic pollination: overall, pollinator exclusion reduced fruit set at harvest to 55% of open pollination levels, whilst supplementary pollination led to fruit set of 167%. However, significant differences were found between the inflorescence, branch, and tree experiments; with increasing scale of observation leading to a lower measure of pollinator-dependence and pollination deficit. At the inflorescence scale, fruit set at harvest was just 13% of normal levels following pollinator exclusion, whilst at the branch and tree scales it was 75% and 79% of normal levels respectively. Supplementary pollination led to fruit set of 218%, 172%, and 117% of normal rates at the inflorescence, branch, and tree scales respectively. Apple seed set was also significantly affected by pollination treatment and the extent of this effect also depended on experimental scale. These differences due to experimental scale are likely a combination of methodological, biological and crop management factors. Seed numbers were shown to be a very good indicator of a number of fruit quality parameters, with greater seed numbers resulting in greater production of Class 1 (i.e. top commercial value) fruit. It is recommended that to measure pollinator-dependence and pollination deficits, experiments are conducted at the largest scale practicable and that treatment effects are monitored until harvest to more accurately reflect final yield outcomes. For apples, growers are recommended to record seed number as part of their fruit quality monitoring programmes to give a rapid and easy to measure indication of potential pollination deficit

Opportunities to reduce pollination deficits and address production shortfalls in an important insect pollinated crop

Pollinators face multiple pressures and there is evidence of populations in decline. As demand for insect-pollinated crops increases, crop production is threatened by shortfalls in pollination services. Understanding the extent of current yield deficits due to pollination and identifying opportunities to protect or improve crop yield and quality through pollination management is therefore of international importance. To explore the extent of ‘pollination deficits’, where maximum yield is not being achieved due to insufficient pollination, we use an extensive dataset on a globally important crop, apples. We quantified how these deficits vary between orchards and countries as well as compare ‘pollinator dependence’ across different apple varieties. We found evidence of pollination deficits and in some cases, risks of over-pollination were even apparent where fruit quality could be reduced by too much pollination. In almost all regions studied we found some orchards performing significantly better than others, in terms of avoiding a pollination deficit and crop yield shortfalls due to sub-optimal pollination. This represents an opportunity to improve production through better pollinator and crop management. Our findings also demonstrate that pollinator dependence varies considerably between apple varieties in terms of fruit number and fruit quality. We propose that assessments of pollination service and deficits in crops can be used to quantify supply and demand for pollinators and help target local management to address deficits although crop variety has a strong influence on the role of pollinators