Iron Uptake and Homeostasis in Microorganisms

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

On defining base units in terms of fundamental constants

The definitions of the base units of the international system of units have been revised many times since the idea of such an international system was first conceived at the time of the French revolution. The objective today is to define all our units in terms of 'invariants of nature', i.e. by referencing our units to the fundamental constants of physics, or the properties of atoms, rather than the characteristics of our planet or of artefacts. This situation is reviewed, particularly in regard to finding a new definition of the kilogram to replace its present definition in terms of a prototype material artefact.

Creating teaching and learning in Europe: promoting a new paradigm

The tides of globalization and the unsteady surges and distortions in the evolution of the European Union are causing identities and cultures to be in a state of flux. Education is used by politicians as a major lever for political and social change through micro-management, but it is a crude tool. There can, however, be opportunities within educational experience for individual learners to gain strong, reflexive, multiple identities and multiple citizenship through the engagement of their creative energies. It has been argued that the twenty-first century needs a new kind of creativity characterized by unselfishness, caring and compassion—still involving monetary wealth, but resulting in a healthy planet and healthy people. Creativity and its economically derived relation, innovation, have become `buzz words' of our times. They are often misconstrued, misunderstood and plainly misused within educational conversations. The small-scale pan-European research study upon which this article is founded discovered that more emphasis needs to be placed on creative leadership, empowering teachers and learners, reducing pupils' fear of school, balancing teaching approaches, and ensuring that the curriculum and assessment are responsive to the needs of individual learners. These factors are key to building strong educational provision that harnesses the creative potential of learners, teachers and other stakeholders, values what it is to be human and creates a foundation upon which to build strong, morally based, consistent, participative democracies.

Aspects of the large scale tropical atmospheric circulation

An account is given of a number of recent studies with idealised models whose aim is to further understanding of the large-scale tropical atmospheric circulation. Initial-value integrations with a model with imposed heating are used to discuss aspects of the Asian summer monsoon, including constraints on cross-equatorial flow into the monsoon. The summer descent in the Mediterranean region and on the eastern sides of the summer subtropical anticyclones are seen to be associated with the monsoons to their east. An aqua-planet GCM is used to investigate the relationship between simple SST distributions and tropical convection and circulation. The existence of strong equatorial convection and Hadley cells is found to depend sensitively on the curvature of the meridional profile in SST. Zonally confined SST maxima produce convective maxima centred to the west and suppression of convection elsewhere. Strong equatorial zonal flow changes are found in some experiments and three mechanisms for producing these are investigated in a model with imposed heating. 1.

Think local, act local? Issues of co-ordination and integration in Local Agenda 21

The political response to the complex package of environmental problems which threaten the future of our planet has been to introduce a new agenda of environmental action based on the principles of sustainability and subsidiarity. This has been crystallised in world agreements signed at the Earth Summit in Rio. One of these, Agenda 21, calls for the governments and communities of the world to prepare action plans for their areas which can build consensus between the various stakeholder groups and feed the principles of sustainable development back into their policies and day-to-day practices. This paper explores the experience of Local Agenda 21 type processes at three levels in the South East of England: the regional, county (sub-regional) and local level. In particular it undertakes a critical appraisal of the success of these participatory and consensus-building exercises in developing an integrated and co-ordinated approach to environmental action planning. It concludes that, although much useful work has been done in raising awareness and modifying policy and practice, there are significant cultural and institutional barriers which are hindering progress.

Cuckoos at Wicken Fen, snow, and radiocarbon dating

This week in the Planet Earth Podcast: the cunning tricks the cuckoo uses to get another bird to do the parenting, why researchers are studying snow in Sweden, and how an improved radiocarbon dating technique may put a few scientists' noses out of joint.

Economists are not dismal, the world is not a Petri dish and other reasons for optimism

One of the recurrent themes in the debate around how to ensure global food security concerns the capacity of the planet to support its growing population. Neo-Malthusian thinking suggests that we are in a situation in which further expansion of the population cannot be supported and that the population checks, with their dismal consequences envisaged by Malthus, will lead to a new era of stagnant incomes and population. More sophisticated models of the link between population and income are less gloomy however. They see population growth as an integral component of the economic growth which is necessary to ensure that the poorest achieve food security. An undue focus on the difficulties of meeting the demands of the increasing population risks damaging this growth. Instead, attention should be focused on ensuring that the conditions to ensure that economic growth accompanies population growth are in place.

Detection and attribution of climate change: a regional perspective

The Intergovernmental Panel on Climate Change fourth assessment report, published in 2007 came to a more confident assessment of the causes of global temperature change than previous reports and concluded that ‘it is likely that there has been significant anthropogenic warming over the past 50 years averaged over each continent except Antarctica.’ Since then, warming over Antarctica has also been attributed to human influence, and further evidence has accumulated attributing a much wider range of climate changes to human activities. Such changes are broadly consistent with theoretical understanding, and climate model simulations, of how the planet is expected to respond. This paper reviews this evidence from a regional perspective to reflect a growing interest in understanding the regional effects of climate change, which can differ markedly across the globe. We set out the methodological basis for detection and attribution and discuss the spatial scales on which it is possible to make robust attribution statements. We review the evidence showing significant human-induced changes in regional temperatures, and for the effects of external forcings on changes in the hydrological cycle, the cryosphere, circulation changes, oceanic changes, and changes in extremes. We then discuss future challenges for the science of attribution. To better assess the pace of change, and to understand more about the regional changes to which societies need to adapt, we will need to refine our understanding of the effects of external forcing and internal variability

Support for global climate reorganization during the "Medieval Climate Anomaly"

Widely distributed proxy records indicate that the Medieval Climate Anomaly (MCA; *900–1350 AD) was characterized by coherent shifts in large-scale Northern Hemisphere atmospheric circulation patterns. Although cooler sea surface temperatures in the central and eastern equatorial Pacific can explain some aspects of medieval circulation changes, they are not sufficient to account for other notable features, including widespread aridity through the Eurasian sub-tropics, stronger winter westerlies across the North Atlantic and Western Europe, and shifts in monsoon rainfall patterns across Africa and South Asia. We present results from a full-physics coupled climate model showing that a slight warming of the tropical Indian and western Pacific Oceans relative to the other tropical ocean basins can induce a broad range of the medieval circulation and climate changes indicated by proxy data, including many of those not explained by a cooler tropical Pacific alone. Important aspects of the results resemble those from previous simulations examining the climatic response to the rapid Indian Ocean warming during the late twentieth century, and to results from climate warming simulations—especially in indicating an expansion of the Northern Hemisphere Hadley circulation. Notably, the pattern of tropical Indo-Pacific sea surface temperature (SST) change responsible for producing the proxy-model similarity in our results agrees well with MCA-LIA SST differences obtained in a recent proxy-based climate field reconstruction. Though much remains unclear, our results indicate that the MCA was characterized by an enhanced zonal Indo-Pacific SST gradient with resulting changes in Northern Hemisphere tropical and extra-tropical circulation patterns and hydroclimate regimes, linkages that may explain the coherent regional climate shifts indicated by proxy records from across the planet. The findings provide new perspectives on the nature and possible causes of the MCA—a remarkable, yet incompletely understood episode of Late Holocene climatic change.

Emerging agricultural hydrology problems in post-conflict Libya

This paper develops a conceptual framework for analyzing emerging agricultural hydrology problems in post-conflict Libya. Libya is one of the most arid regions on the planet. Thus, as well as substantial political and social changes, post-conflict Libyan administrators are confronted with important hydrological issues in Libya’s emerging water-landuse complex. This paper presents a substantial background to the water-land-use problem in Libya; reviews previous work in Libya and elsewhere on water-land-use issues and water-land-use conflicts in the dry and arid zones; outlines a conceptual framework for fruitful research interventions; and details the results of a survey conducted on Libyan farmers’ water usage, perceptions of emerging water-land-use conflicts and the appropriate value one should place on agricultural-use hydrological resources in Libya. Extensions are discussed.

Making robust policy decision using global biodiversity indicators

In order to influence global policy effectively, conservation scientists need to be able to provide robust predictions of the impact of alternative policies on biodiversity and measure progress towards goals using reliable indicators. We present a framework for using biodiversity indicators predictively to inform policy choices at a global level. The approach is illustrated with two case studies in which we project forwards the impacts of feasible policies on trends in biodiversity and in relevant indicators. The policies are based on targets agreed at the Convention on Biological Diversity (CBD) meeting in Nagoya in October 2010. The first case study compares protected area policies for African mammals, assessed using the Red List Index; the second example uses the Living Planet Index to assess the impact of a complete halt, versus a reduction, in bottom trawling. In the protected areas example, we find that the indicator can aid in decision-making because it is able to differentiate between the impacts of the different policies. In the bottom trawling example, the indicator exhibits some counter-intuitive behaviour, due to over-representation of some taxonomic and functional groups in the indicator, and contrasting impacts of the policies on different groups caused by trophic interactions. Our results support the need for further research on how to use predictive models and indicators to credibly track trends and inform policy. To be useful and relevant, scientists must make testable predictions about the impact of global policy on biodiversity to ensure that targets such as those set at Nagoya catalyse effective and measurable change.

The APE atlas

This Atlas presents statistical analyses of the simulations submitted to the Aqua-Planet Experiment (APE) data archive. The simulations are from global Atmospheric General Circulation Models (AGCM) applied to a water-covered earth. The AGCMs include ones actively used or being developed for numerical weather prediction or climate research. Some are mature, application models and others are more novel and thus less well tested in Earth-like applications. The experiment applies AGCMs with their complete parameterization package to an idealization of the planet Earth which has a greatly simplified lower boundary that consists of an ocean only. It has no land and its associated orography, and no sea ice. The ocean is represented by Sea Surface Temperatures (SST) which are specified everywhere with simple, idealized distributions. Thus in the hierarchy of tests available for AGCMs, APE falls between tests with simplified forcings such as those proposed by Held and Suarez (1994) and Boer and Denis (1997) and Earth-like simulations of the Atmospheric Modeling Intercomparison Project (AMIP, Gates et al., 1999). Blackburn and Hoskins (2013) summarize the APE and its aims. They discuss where the APE fits within a modeling hierarchy which has evolved to evaluate complete models and which provides a link between realistic simulation and conceptual models of atmospheric phenomena. The APE bridges a gap in the existing hierarchy. The goals of APE are to provide a benchmark of current model behaviors and to stimulate research to understand the cause of inter-model differences., APE is sponsored by the World Meteorological Organization (WMO) joint Commission on Atmospheric Science (CAS), World Climate Research Program (WCRP) Working Group on Numerical Experimentation (WGNE). Chapter 2 of this Atlas provides an overview of the specification of the eight APE experiments and of the data collected. Chapter 3 lists the participating models and includes brief descriptions of each. Chapters 4 through 7 present a wide variety of statistics from the 14 participating models for the eight different experiments. Additional intercomparison figures created by Dr. Yukiko Yamada in AGU group are available at http://www.gfd-dennou.org/library/ape/comparison/. This Atlas is intended to present and compare the statistics of the APE simulations but does not contain a discussion of interpretive analyses. Such analyses are left for journal papers such as those included in the Special Issue of the Journal of the Meteorological Society of Japan (2013, Vol. 91A) devoted to the APE. Two papers in that collection provide an overview of the simulations. One (Blackburn et al., 2013) concentrates on the CONTROL simulation and the other (Williamson et al., 2013) on the response to changes in the meridional SST profile. Additional papers provide more detailed analysis of the basic simulations, while others describe various sensitivities and applications. The APE experiment data base holds a wealth of data that is now publicly available from the APE web site: http://climate.ncas.ac.uk/ape/. We hope that this Atlas will stimulate future analyses and investigations to understand the large variation seen in the model behaviors.

The global atmospheric water cycle

Water vapour plays a key role in the Earth's energy balance. Almost 50% of the absorbed solar radiation at the surface is used to cool the surface, through evaporation, and warm the atmosphere, through release of latent heat. Latent heat is the single largest factor in warming the atmosphere and in transporting heat from low to high latitudes. Water vapour is also the dominant greenhouse gas and contributes to a warming of the climate system by some 24°C (Kondratev 1972). However, water vapour is a passive component in the troposphere as it is uniquely determined by temperature and should therefore be seen as a part of the climate feedback system. In this short overview, we will first describe the water on planet Earth and the role of the hydrological cycle: the way water vapour is transported between oceans and continents and the return of water via rivers to the oceans. Generally water vapour is well observed and analysed; however, there are considerable obstacles to observing precipitation, in particular over the oceans. The response of the hydrological cycle to global warming is far reaching. Because different physical processes control the change in water vapour and evaporation/precipitation, this leads to a more extreme distribution of precipitation making, in general, wet areas wetter and dry areas dryer. Another consequence is a transition towards more intense precipitation. It is to be expected that the changes in the hydrological cycle as a consequence of climate warming may be more severe that the temperature changes.

Towards understanding the climate of Venus

ESA’s Venus Express Mission has monitored Venus since April 2006, and scientists worldwide have used mathematical models to investigate its atmosphere and model its circulation. This book summarizes recent work to explore and understand the climate of the planet through a research program under the auspices of the International Space Science Institute (ISSI) in Bern, Switzerland. Some of the unique elements that are discussed are the anomalies with Venus’ surface temperature (the huge greenhouse effect causes the surface to rise to 460°C, without which would plummet as low as -40°C), its unusual lack of solar radiation (despite being closer to the Sun, Venus receives less solar radiation than Earth due to its dense cloud cover reflecting 76% back) and the juxtaposition of its atmosphere and planetary rotation (wind speeds can climb up to 200 m/s, much faster than Venus’ sidereal day of 243 Earth-days).