Plant conservation in space, time and a changing world: forecasting the fate of Coffea arabica in Ethiopia

We are facing an ever-increasing environmental crisis on our planet, with multiple threats from humankind. Industrialisation, deforestation, overpopulation and exploitation of our natural resources is driving species to extinction and changing the environment we live in. We need to plan for the future in order to adapt or mitigate these risks. Recent advances in computing and analytical techniques, plus the rise of readily available spatial data, provide us with a means to understand the complex interactions between species, environmental change and human activity. Coffea arabica (Arabica coffee) is a critically important crop species in several tropical countries. Globally its export value is over $13 billion dollars per year. Wild populations of this species are of immense importance to the global coffee sector, due to the traits associated with the standing genetic diversity, such as disease resilience, new flavour profiles, and agronomically favourable morphological variation (root length; compact habit). In its countries of origin, Ethiopia and South Sudan, the wild species provides the planting stock for a multi-million-dollar export sector. Arabica coffee is well known across the globe, as the increasingly popular beverage coffee. The ubiquitous cultural nature of coffee drinking means that coffee acts as a flagship species for demonstrating science and the benefits of conservation and sustainable use, enabling the findings of this thesis to gain traction with a wider audience, who might otherwise not engage with research and social and environmental issues. Coffea arabica is greatly influenced by climate. The wild and cultivated variants of this species are restricted to a relatively narrow climate niche, within Ethiopia and anywhere where it is cultivated. Coffee production is considerably influenced by changes in rainfall, temperature or seasonality. Ethiopia has already experienced climate change; mean temperatures from the 1960s onwards show an average increase of 0.28 °C per decade, a shortening wet season, and an increase in the number of hot days. The continuation of this rapid change in climate will influence both wild populations and production of Arabica coffee in Ethiopia. Within this thesis I forecast the fate of wild and cultivated Arabica coffee in Ethiopia, under climate change, reviewing risks and opportunities from the recent past until the end of the century. To do this I developed several novel methods, which are initially used to project the future of wild and cultivated coffee cultivation in Ethiopia. For the wild species, I have developed several new spatial techniques, particularly dealing with the issue of the “modifiable areal unit problem” within species extinction risk assessments. I have updated and refined existing techniques into one package, allowing multiple future climate scenarios/projections to be processed and assessed quickly. I present my scientific findings in the form of five submitted manuscripts (see ‘List of original articles’, on p.8). Using the findings, results and recommendations from these papers, I repurpose the outputs and impact of the science, graphically and within various media (including two more manuscripts, media and social media), for multiple audiences. Using these spatial techniques and visualisations, I show the impact climate change will have on Arabica coffee in Ethiopia, both as a crop and as a wild species within the humid forests of the country. I show that the present coffee-growing areas could be reduced by up to 60% if no interventions are made, but conversely, that there is an opportunity to increase the coffee growing area of Ethiopia four-fold if the right actions are taken. For wild Arabica coffee I show that the species is threatened with extinction due to climate change. Specifically, I show that wild Arabica coffee would be assessed as Least Concern (under little or no risk; IUCN Extinction Red List) if climate change is not factored in, as opposed to Endangered (threatened with extinction) if climate change is included in an extinction risk assessment. The work in this thesis demonstrates the power of spatial analysis, modelling, and high data quality, for plant conservation

Ecología y diagnóstico de Enallodiplosis discordis (Diptera:Cecidomyiidae): Un nuevo defoliador feroz con repercusiones directas en la pérdida del bosque seco de Prosopis y los medios de vida en Perú

The coastal desert of Peru and Chile is home to Prosopis (Leguminosae: Mimosoideae) tree species that are exceptionally well-adapted to the hyperarid conditions and keystone in dry-forest ecosystems. From 2001 to 2018, Prosopis in Peru have suffered widespread defoliation and die-back, with consequent deforestation and collapse in pod production. This paper reports a new insect plague species of Prosopis forest in Peru: Enallodiplosis discordis Gagné 1994 (Diptera: Cecidomyiidae) as a fiercely defoliating agent contributing to widespread Prosopis mortality. An analysis of E. discordis larval taxonomy, life cycle and plague infestation, following El Niño Southern Oscillation (ENSO) 1998/99 is provided. Using distinct lines of evidence, its spread, distribution, and ecology are examined. Over two decades of fieldwork, Prosopis forest die-back and loss was observed devastating rural livelihoods and ecosystem services across lowland regions of southern (Ica), central and northern coastal Peru (Lambayeque, La Libertad, Piura). The collapse in production of Prosopis pods (algarroba, huaranga) and honey was recorded. Supplementary notes provide observations of: (i) plague development, changing land-use and climate, (ii) biological and physical control of E. discordis, (iii) the moth Melipotis aff. indomita (Lepidoptera: Noctuidae) as a concurrent defoliator of Prosopis.Las regiones desérticas costeras del Pacífico de Perú y Chile albergan especies de Prosopis (Leguminosae: Mimosoideae), árboles bien adaptados a las condiciones del desierto y con funciones clave en los ecosistemas de bosques secos. Entre el 2001 y 2017, Prosopis en Perú ha sufrido una extensiva defoliación y muerte regresiva, con la consecuente deforestación y disminución de la producción de vainas de algarrobo. Aquí, se reporta una nueva especie de insecto plaga del bosque de Prosopis en Perú: Enallodiplosis discordis Gagné 1994 (Diptera: Cecidomyiidae), una feroz especie defoliadora que contribuye a la mortalidad generalizada de Prosopis. Se proporciona un análisis de la taxonomía larvaria de E. discordis, ciclo de vida y la infestación ocurrida después de El Niño Oscilación del Sur (ENSO) 1998/99. Su dispersión, distribución y ecología es examinada utilizando distintas líneas de evidencia. Durante casi dos décadas de trabajo de campo, se observó la muerte regresiva del bosque de Prosopis devastando los medios de vida rurales y los servicios de los ecosistemas en las regiones de las tierras bajas del sur (Ica), el centro y el norte de la costa peruana (Lambayeque, La Libertad, Piura). El colapso en la producción de vainas de Prosopis (algarroba, huaranga) y miel también fue registrada. Las notas complementarias proporcionan observaciones sobre: (i) el desarrollo de la plaga y el cambio de uso de la tierra y el clima, (ii) el control biológico y físico de E. discordis, (iii) la polilla Melipotis aff. indomita (Lepidoptera: Noctuidae) como defoliador concurrente de Prosopis

Processes, contexts, and rationale for disinvestment: a protocol for a critical interpretive synthesis

Background: Practical solutions are needed to support the appropriate use of available health system resources as countries are continually pressured to ‘do more with less’ in health care. Increasingly, health systems and organizations are exploring the reassessment of possibly obsolete, inefficient, or ineffective health system resources and potentially redirecting funds to those that are more effective and efficient. Such processes are often referred to as ‘disinvestment’. Our objective is to gain further understanding about: 1) whether how and under what conditions health systems decide to pursue disinvestment; 2) how health systems have chosen to undertake disinvestment; and 3) how health systems have implemented their disinvestment approach. Methods/Design We will use a critical interpretive synthesis (CIS) approach, to develop a theoretical framework based on insights drawn from a range of relevant sources. We will conduct systematic searches of databases as well as purposive searches to identify literature to fill conceptual gaps that may emerge during our inductive process of synthesis and analysis. Two independent reviewers will assess search results for relevance and conceptually map included references. We will include all empirical and non-empirical articles that focus on disinvestment at a system level. We will then extract key findings from a purposive sample of articles using frameworks related to government agendas, policy development and implementation, and health system contextual factors and then synthesize and integrate the findings to develop a framework about our core areas of interest. Lastly, we will convene a stakeholder dialogue with Canadian and international policymakers and other stakeholders to solicit targeted feedback about the framework (e.g., by identifying any gaps in the literature that we may want to revisit before finalizing it) and deliberating about barriers for developing and implementing approaches to disinvestment, strategies to address these barriers and about next steps that could be taken by different constituencies. Discussion Disinvestment is an emerging field and there is a need for evidence to inform the prioritization, development, and implementation of strategies in different contexts. Our CIS and the framework developed through it will support the actions of those involved in the prioritization, development, and implementation of disinvestment initiatives. Systematic review registration PROSPERO CRD42014013204 Electronic supplementary material The online version of this article (doi:10.1186/2046-4053-3-143) contains supplementary material, which is available to authorized users

Rapid forest inventory and mapping: Monitoring forest cover and land use change

This paper discusses the research tools used to create baseline data for carbon offset mechanisms. The paper explains vegetation survey methodologies with examples of their application in a variety of contexts. These range from rapid studies using remote sensing imagery, to full multiphase survey methods. The paper gives specific examples of how these methods are used to monitor deforestation and forest regeneration

Gymnosperms on the EDGE

Driven by limited resources and a sense of urgency, the prioritization of species for conservation has been a persistent concern in conservation science. Gymnosperms (comprising ginkgo, conifers, cycads, and gnetophytes) are one of the most threatened groups of living organisms, with 40% of the species at high risk of extinction, about twice as many as the most recent estimates for all plants (i.e. 21.4%). This high proportion of species facing extinction highlights the urgent action required to secure their future through an objective prioritization approach. The Evolutionary Distinct and Globally Endangered (EDGE) method rapidly ranks species based on their evolutionary distinctiveness and the extinction risks they face. EDGE is applied to gymnosperms using a phylogenetic tree comprising DNA sequence data for 85% of gymnosperm species (923 out of 1090 species), to which the 167 missing species were added, and IUCN Red List assessments available for 92% of species. The effect of different extinction probability transformations and the handling of IUCN data deficient species on the resulting rankings is investigated. Although top entries in our ranking comprise species that were expected to score well (e.g. Wollemia nobilis, Ginkgo biloba), many were unexpected (e.g. Araucaria araucana). These results highlight the necessity of using approaches that integrate evolutionary information in conservation science

Innovative approaches to the preservation of forest trees

AbstractThe recent acceleration of actions to conserve plant species using ex situ and in situ strategies has revealed the need to understand how these two approaches might be better developed and integrated in their application to tree species. Here we review some of the recent successes relating mainly to tree seed biology that have resulted in the development and application of innovative actions across five areas: (i) the expansion of living collections to conserve threatened tree species in sufficient numbers to ensure a broad genetic diversity in their progeny; (ii) the generation of viability constants to enable estimates to be made of storage longevity of tree seeds in the dry state; (iii) improvement in the diagnosis of tree seed storage behaviour through the development of predictive models, reliable prognoses of desiccation tolerance and use of botanical information systems, such as GIS, to correlate information on species distribution and their physiological characteristics; (iv) advances in storage preservation biotechnology to enhance the future application of cryopreservation procedures to recalcitrant species in biodiversity hotspots where many are under threat of extinction; and (v) integration of ex situ and in situ conservation approaches to ensure that best practice in horticultural and forestry are combined to maintain or enhance genetic diversity, especially in high value species and those with small and vulnerable populations. These actions can lead to greater impact if supported by greater efforts to create seed banks and to collate databases world-wide so that data, knowledge and collections are more available to the scientific, forestry and NGO communities. Throughout this review we have used examples from the mega-biodiversity countries of Brazil and China, as a way of illustrating wider principles that can be applied in many countries. Future development of current research approaches, the adherence to conservation policy and the expanding needs for education are also considered briefly

Model-observation and reanalyses comparison at key locations for heat transport to the Arctic: Assessment of key lower latitude influences on the Arctic and their simulation

Blue-Action Work Package 2 (WP2) focuses on lower latitude drivers of Arctic change, with a focus on the influence of the Atlantic Ocean and atmosphere on the Arctic. In particular, warm water travels from the Atlantic, across the Greenland-Scotland ridge, through the Norwegian Sea towards the Arctic. A large proportion of the heat transported northwards by the ocean is released to the atmosphere and carried eastward towards Europe by the prevailing westerly winds. This is an important contribution to northwestern Europe's mild climate. The remaining heat travels north into the Arctic. Variations in the amount of heat transported into the Arctic will influence the long term climate of the Northern Hemisphere. Here we assess how well the state of the art coupled climate models estimate this northwards transport of heat in the ocean, and how the atmospheric heat transport varies with changes in the ocean heat transport. We seek to improve the ocean monitoring systems that are in place by introducing measurements from ocean gliders, Argo floats and satellites. These state of the art computer simulations are evaluated by comparison with key trans-Atlantic observations. In addition to the coupled models ‘ocean-only’ evaluations are made. In general the coupled model simulations have too much heat going into the Arctic region and the transports have too much variability. The models generally reproduce the variability of the Atlantic Meridional Ocean Circulation (AMOC) well. All models in this study have a too strong southwards transport of freshwater at 26°N in the North Atlantic, but the divergence between 26°N and Bering Straits is generally reproduced really well in all the models. Altimetry from satellites have been used to reconstruct the ocean circulation 26°N in the Atlantic, over the Greenland Scotland Ridge and alongside ship based observations along the GO-SHIP OVIDE Section. Although it is still a challenge to estimate the ocean circulation at 26°N without using the RAPID 26°N array, satellites can be used to reconstruct the longer term ocean signal. The OSNAP project measures the oceanic transport of heat across a section which stretches from Canada to the UK, via Greenland. The project has used ocean gliders to great success to measure the transport on the eastern side of the array. Every 10 days up to 4000 Argo floats measure temperature and salinity in the top 2000m of the ocean, away from ocean boundaries, and report back the measurements via satellite. These data are employed at 26°N in the Atlantic to enable the calculation of the heat and freshwater transports. As explained above, both ocean and atmosphere carry vast amounts of heat poleward in the Atlantic. In the long term average the Atlantic ocean releases large amounts of heat to the atmosphere between the subtropical and subpolar regions, heat which is then carried by the atmosphere to western Europe and the Arctic. On shorter timescales, interannual to decadal, the amounts of heat carried by ocean and atmosphere vary considerably. An important question is whether the total amount of heat transported, atmosphere plus ocean, remains roughly constant, whether significant amounts of heat are gained or lost from space and how the relative amount transported by the atmosphere and ocean change with time. This is an important distinction because the same amount of anomalous heat transport will have very different effects depending on whether it is transported by ocean or the atmosphere. For example the effects on Arctic sea ice will depend very much on whether the surface of the ice experiences anomalous warming by the atmosphere versus the base of the ice experiencing anomalous warming from the ocean. In Blue-Action we investigated the relationship between atmospheric and oceanic heat transports at key locations corresponding to the positions of observational arrays (RAPID at 26°N, OSNAP at ~55N, and the Denmark Strait, Iceland-Scotland Ridge and Davis Strait at ~67N) in a number of cutting edge high resolution coupled ocean-atmosphere simulations. We split the analysis into two different timescales, interannual to decadal (1-10 years) and multidecadal (greater than 10 years). In the 1-10 year case, the relationship between ocean and atmosphere transports is complex, but a robust result is that although there is little local correlation between oceanic and atmospheric heat transports, Correlations do occur at different latitudes. Thus increased oceanic heat transport at 26°N is accompanied by reduced heat transport at ~50N and a longitudinal shift in the location of atmospheric flow of heat into the Arctic. Conversely, on longer timescales, there appears to be a much stronger local compensation between oceanic and atmospheric heat transport i.e. Bjerknes compensation

Plant Power:Opportunities and challenges for meeting sustainable energy needs from the plant and fungal kingdoms

Societal Impact Statement Bioenergy is a major component of the global transition to renewable energy technologies. The plant and fungal kingdoms offer great potential but remain mostly untapped. Their increased use could contribute to the renewable energy transition and addressing the United Nations Sustainable Development Goal 7 “Ensure access to affordable, reliable, sustainable and modern energy for all.” Current research focuses on species cultivated at scale in temperate regions, overlooking the wealth of potential new sources of small‐scale energy where they are most urgently needed. A shift towards diversified, accessible bioenergy technologies will help to mitigate and adapt to the threats of climate change, decrease energy poverty, improve human health by reducing indoor pollution, increase energy resilience of communities, and decrease greenhouse gas emissions from fossil fuels. Summary Bioenergy derived from plants and fungi is a major component of the global transition to renewable energy technologies. There is rich untapped diversity in the plant and fungal kingdoms that offers potential to contribute to the shift away from fossil fuels and to address the United Nations Sustainable Development Goal 7 (SDG7) “Ensure access to affordable, reliable, sustainable and modern energy for all.” Energy poverty—the lack of access to modern energy services—is most acute in the Global South where biodiversity is greatest and least investigated. Our systematic review of the literature over the last 5 years (2015–2020) indicates that research efforts have targeted a very small number of plant species cultivated at scale, mostly in temperate regions. The wealth of potential new sources of bioenergy in biodiverse regions, where the implementation of SDG7 is most urgently needed, has been largely overlooked. We recommend next steps for bioenergy stakeholders—research, industry, and government—to seize opportunities for innovation to alleviate energy poverty while protecting biodiversity. Small‐scale energy production using native plant species in bioenergy landscapes overcomes many pitfalls associated with bioenergy crop monocultures, such as biodiversity loss and conflict with food production. Targeted trait‐based screening of plant species and biological screening of fungi are required to characterize the potential of this resource. The benefits of diversified, accessible bioenergy go beyond the immediate urgency of energy poverty as more diverse agricultural landscapes are more resilient, store more carbon, and could also reduce the drivers of the climate and environmental emergencies

Correction: Metal complexes as a promising source for new antibiotics

Correction for ‘Metal complexes as a promising source for new antibiotics’ by Angelo Frei et al., Chem. Sci., 2020, 11, 2627–2639

Metal complexes as a promising source for new antibiotics

There is a dire need for new antimicrobial compounds to combat the growing threat of widespread antibiotic resistance. With a currently very scarce drug pipeline, consisting mostly of derivatives of known antibiotics, new classes of antibiotics are urgently required. Metal complexes are currently in clinical development for the treatment of cancer, malaria and neurodegenerative diseases. However, only little attention has been paid to their application as potential antimicrobial compounds. We report the evaluation of 906 metal-containing compounds that have been screened by the Community for Open Antimicrobial Drug Discovery (CO-ADD) for antimicrobial activity. Metal-bearing compounds display a significantly higher hit-rate (9.9%) when compared to the purely organic molecules (0.87%) in the CO-ADD database. Out of 906 compounds, 88 show activity against at least one of the tested strains, including fungi, while not displaying any cytotoxicity against mammalian cell lines or haemolytic properties. Herein, we highlight the structures of the 30 compounds with activity against Gram-positive and/or Gram-negative bacteria containing Mn, Co, Zn, Ru, Ag, Eu, Ir and Pt, with activities down to the nanomolar range against methicillin resistant S. aureus (MRSA). 23 of these complexes have not been reported for their antimicrobial properties before. This work reveals the vast diversity that metal-containing compounds can bring to antimicrobial research. It is important to raise awareness of these types of compounds for the design of truly novel antibiotics with potential for combatting antimicrobial resistance