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

An assessment of the fine sediment dynamics in an upland river system: INCA-Sed modifications and implications for fisheries

There is a need for better links between hydrology and ecology, specifically between landscapes and riverscapes to understand how processes and factors controlling the transport and storage of environmental pollution have affected or will affect the freshwater biota. Here we show how the INCA modelling framework, specifically INCA-Sed (the Integrated Catchments model for Sediments) can be used to link sediment delivery from the landscape to sediment changes in-stream. INCA-Sed is a dynamic, process-based, daily time step model. The first complete description of the equations used in the INCA-Sed software (version 1.9.11) is presented. This is followed by an application of INCA-Sed made to the River Lugg (1077 km2) in Wales. Excess suspended sediment can negatively affect salmonid health. The Lugg has a large and potentially threatened population of both Atlantic salmon (Salmo salar) and Brown Trout (Salmo trutta). With the exception of the extreme sediment transport processes, the model satisfactorily simulated both the hydrology and the sediment dynamics in the catchment. Model results indicate that diffuse soil loss is the most important sediment generation process in the catchment. In the River Lugg, the mean annual Guideline Standard for suspended sediment concentration, proposed by UKTAG, of 25 mg l− 1 is only slightly exceeded during the simulation period (1995–2000), indicating only minimal effect on the Atlantic salmon population. However, the daily time step simulation of INCA-Sed also allows the investigation of the critical spawning period. It shows that the sediment may have a significant negative effect on the fish population in years with high sediment runoff. It is proposed that the fine settled particles probably do not affect the salmonid egg incubation process, though suspended particles may damage the gills of fish and make the area unfavourable for spawning if the conditions do not improve.

Link between DOC in near surface peat and stream water in an upland catchment

Hydrologic transport of dissolved organic carbon (DOC) from peat soils may differ to organo-mineral soils in how they responded to changes in flow, because of differences in soil profile and hydrology. In well-drained organo-mineral soils, low flow is through the lower mineral layer where DOC is absorbed and high flow is through the upper organic layer where DOC is produced. DOC concentrations in streams draining organo-mineral soils typically increase with flow. In saturated peat soils, both high and low flows are through an organic layer where DOC is produced. Therefore, DOC in stream water draining peat may not increase in response to changes in flow as there is no switch in flow path between a mineral and organic layer. To verify this, we conducted a high-resolution monitoring study of soil and stream water at an upland peat catchment in northern England. Our data showed a strong positive correlation between DOC concentrations at − 1 and − 5 cm depth and stream water, and weaker correlations between concentrations at − 20 to − 50 cm depth and stream water. Although near surface organic material appears to be the key source of stream water DOC in both peat and organo-mineral soils, we observed a negative correlation between stream flow and DOC concentrations instead of a positive correlation as DOC released from organic layers during low and high flow was diluted by rainfall. The differences in DOC transport processes between peat and organo-mineral soils have different implications for our understanding of long-term changes in DOC exports. While increased rainfall may cause an increase in DOC flux from peat due to an increase in water volume, it may cause a decrease in concentrations. This response is contrary to expected changes in DOC exports from organo-mineral soils, where increase rainfall is likely to result in an increase in flux and concentration.

Thermodynamic analysis of snowball Earth hysteresis experiment: Efficiency, entropy production and irreversibility

We present an extensive thermodynamic analysis of a hysteresis experiment performed on a simplified yet Earth-like climate model. We slowly vary the solar constant by 20% around the present value and detect that for a large range of values of the solar constant the realization of snowball or of regular climate conditions depends on the history of the system. Using recent results on the global climate thermodynamics, we show that the two regimes feature radically different properties. The efficiency of the climate machine monotonically increases with decreasing solar constant in present climate conditions, whereas the opposite takes place in snowball conditions. Instead, entropy production is monotonically increasing with the solar constant in both branches of climate conditions, and its value is about four times larger in the warm branch than in the corresponding cold state. Finally, the degree of irreversibility of the system, measured as the fraction of excess entropy production due to irreversible heat transport processes, is much higher in the warm climate conditions, with an explosive growth in the upper range of the considered values of solar constants. Whereas in the cold climate regime a dominating role is played by changes in the meridional albedo contrast, in the warm climate regime changes in the intensity of latent heat fluxes are crucial for determining the observed properties. This substantiates the importance of addressing correctly the variations of the hydrological cycle in a changing climate. An interpretation of the climate transitions at the tipping points based upon macro-scale thermodynamic properties is also proposed. Our results support the adoption of a new generation of diagnostic tools based on the second law of thermodynamics for auditing climate models and outline a set of parametrizations to be used in conceptual and intermediate-complexity models or for the reconstruction of the past climate conditions. Copyright © 2010 Royal Meteorological Society

Vertical heat transports in the ocean and their effect on time-dependent climate change

In response to increasing atmospheric con- centrations of greenhouse gases, the rate of time- dependent climate change is determined jointly by the strength of climate feedbacks and the e�ciency of pro- cesses which remove heat from the surface into the deep ocean. This work examines the vertical heat transport processes in the ocean of the HADCM2 atmosphere± ocean general circulation model (AOGCM) in experi- ments with CO2 held constant (control) and increasing at 1% per year (anomaly). The control experiment shows that global average heat exchanges between the upper and lower ocean are dominated by the Southern Ocean, where heat is pumped downwards by the wind- driven circulation and di�uses upwards along sloping isopycnals. This is the reverse of the low-latitude balance used in upwelling±di�usion ocean models, the global average upward di�usive transport being against the temperature gradient. In the anomaly experiment, weakened convection at high latitudes leads to reduced diffusive and convective heat loss from the deep ocean, and hence to net heat uptake, since the advective heat input is less a�ected. Reduction of deep water produc- tion at high latitudes results in reduced upwelling of cold water at low latitudes, giving a further contribution to net heat uptake. On the global average, high-latitude processes thus have a controlling in¯uence. The impor- tant role of di�usion highlights the need to ensure that the schemes employed in AOGCMs give an accurate representation of the relevant sub-grid-scale processes.

Extended magnetic reconnection across the dayside magnetopause

The extent of where magnetic reconnection (MR), the dominant process responsible for energy and plasma transport into the magnetosphere, operates across Earth’s dayside magnetopause has previously been only indirectly shown by observations. We report the first direct evidence of X-line structure resulting from the operation of MR at each of two widely separated locations along the tilted, subsolar line of maximum current on Earth’s magnetopause, confirming the operation of MR at two or more sites across the extended region where MR is expected to occur. The evidence results from in-situ observations of the associated ion and electron plasma distributions, present within each magnetic X-line structure, taken by two spacecraft passing through the active MR regions simultaneously.

Wave activity in the tropical tropopause layer in seven reanalysis and four chemistry climate model data sets

Sub-seasonal variability including equatorial waves significantly influence the dehydration and transport processes in the tropical tropopause layer (TTL). This study investigates the wave activity in the TTL in 7 reanalysis data sets (RAs; NCEP1, NCEP2, ERA40, ERA-Interim, JRA25, MERRA, and CFSR) and 4 chemistry climate models (CCMs; CCSRNIES, CMAM, MRI, and WACCM) using the zonal wave number-frequency spectral analysis method with equatorially symmetric-antisymmetric decomposition. Analyses are made for temperature and horizontal winds at 100 hPa in the RAs and CCMs and for outgoing longwave radiation (OLR), which is a proxy for convective activity that generates tropopause-level disturbances, in satellite data and the CCMs. Particular focus is placed on equatorial Kelvin waves, mixed Rossby-gravity (MRG) waves, and the Madden-Julian Oscillation (MJO). The wave activity is defined as the variance, i.e., the power spectral density integrated in a particular zonal wave number-frequency region. It is found that the TTL wave activities show significant difference among the RAs, ranging from ∼0.7 (for NCEP1 and NCEP2) to ∼1.4 (for ERA-Interim, MERRA, and CFSR) with respect to the averages from the RAs. The TTL activities in the CCMs lie generally within the range of those in the RAs, with a few exceptions. However, the spectral features in OLR for all the CCMs are very different from those in the observations, and the OLR wave activities are too low for CCSRNIES, CMAM, and MRI. It is concluded that the broad range of wave activity found in the different RAs decreases our confidence in their validity and in particular their value for validation of CCM performance in the TTL, thereby limiting our quantitative understanding of the dehydration and transport processes in the TTL.

Transit times – the link between hydrology and water quality at the catchment scale

In spite of trying to understand processes in the same spatial domain, the catchment hydrology and water quality scientific communities are relatively disconnected and so are their respective models. This is emphasized by an inadequate representation of transport processes, in both catchment-scale hydrological and water quality models. While many hydrological models at the catchment scale only account for pressure propagation and not for mass transfer, catchment scale water quality models are typically limited by overly simplistic representations of flow processes. With the objective of raising awareness for this issue and outlining potential ways forward we provide a non-technical overview of (1) the importance of hydrology-controlled transport through catchment systems as the link between hydrology and water quality; (2) the limitations of current generation catchment-scale hydrological and water quality models; (3) the concept of transit times as tools to quantify transport and (4) the benefits of transit time based formulations of solute transport for catchment-scale hydrological and water quality models. There is emerging evidence that an explicit formulation of transport processes, based on the concept of transit times has the potential to improve the understanding of the integrated system dynamics of catchments and to provide a stronger link between catchment-scale hydrological and water quality models.

Processes influencing ozone levels in Alaskan forest fire plumes during long-range transport over the North Atlantic

A case of long-range transport of a biomass burning plume from Alaska to Europe is analyzed using a Lagrangian approach. This plume was sampled several times in the free troposphere over North America, the North Atlantic and Europe by three different aircraft during the IGAC Lagrangian 2K4 experiment which was part of the ICARTT/ITOP measurement intensive in summer 2004. Measurements in the plume showed enhanced values of CO, VOCs and NOy, mainly in form of PAN. Observed O3 levels increased by 17 ppbv over 5 days. A photochemical trajectory model, CiTTyCAT, was used to examine processes responsible for the chemical evolution of the plume. The model was initialized with upwind data and compared with downwind measurements. The influence of high aerosol loading on photolysis rates in the plume was investigated using in situ aerosol measurements in the plume and lidar retrievals of optical depth as input into a photolysis code (Fast-J), run in the model. Significant impacts on photochemistry are found with a decrease of 18% in O3 production and 24% in O3 destruction over 5 days when including aerosols. The plume is found to be chemically active with large O3 increases attributed primarily to PAN decomposition during descent of the plume toward Europe. The predicted O3 changes are very dependent on temperature changes during transport and also on water vapor levels in the lower troposphere which can lead to O3 destruction. Simulation of mixing/dilution was necessary to reproduce observed pollutant levels in the plume. Mixing was simulated using background concentrations from measurements in air masses in close proximity to the plume, and mixing timescales (averaging 6.25 days) were derived from CO changes. Observed and simulated O3/CO correlations in the plume were also compared in order to evaluate the photochemistry in the model. Observed slopes change from negative to positive over 5 days. This change, which can be attributed largely to photochemistry, is well reproduced by multiple model runs even if slope values are slightly underestimated suggesting a small underestimation in modeled photochemical O3 production. The possible impact of this biomass burning plume on O3 levels in the European boundary layer was also examined by running the model for a further 5 days and comparing with data collected at surface sites, such as Jungfraujoch, which showed small O3 increases and elevated CO levels. The model predicts significant changes in O3 over the entire 10 day period due to photochemistry but the signal is largely lost because of the effects of dilution. However, measurements in several other BB plumes over Europe show that O3 impact of Alaskan fires can be potentially significant over Europe.

Quantification of chemical and physical processes influencing ozone during long-range transport using a trajectory ensemble

During long-range transport, many distinct processes – including photochemistry, deposition, emissions and mixing – contribute to the transformation of air mass composition. Partitioning the effects of different processes can be useful when considering the sensitivity of chemical transformation to, for example, a changing environment or anthropogenic influence. However, transformation is not observed directly, since mixing ratios are measured, and models must be used to relate changes to processes. Here, four cases from the ITCT-Lagrangian 2004 experiment are studied. In each case, aircraft intercepted a distinct air mass several times during transport over the North Atlantic, providing a unique dataset and quantifying the net changes in composition from all processes. A new framework is presented to deconstruct the change in O3 mixing ratio (Δ O3) into its component processes, which were not measured directly, taking into account the uncertainty in measurements, initial air mass variability and its time evolution. The results show that the net chemical processing (Δ O3chem) over the whole simulation is greater than net physical processing (Δ O3phys) in all cases. This is in part explained by cancellation effects associated with mixing. In contrast, each case is in a regime of either net photochemical destruction (lower tropospheric transport) or production (an upper tropospheric biomass burning case). However, physical processes influence O3 indirectly through addition or removal of precursor gases, so that changes to physical parameters in a model can have a larger effect on Δ O3chem than Δ O3phys. Despite its smaller magnitude, the physical processing distinguishes the lower tropospheric export cases, since the net photochemical O3 change is −5 ppbv per day in all three cases. Processing is quantified using a Lagrangian photochemical model with a novel method for simulating mixing through an ensemble of trajectories and a background profile that evolves with them. The model is able to simulate the magnitude and variability of the observations (of O3, CO, NOy and some hydrocarbons) and is consistent with the time-average OH following air-masses inferred from hydrocarbon measurements alone (by Arnold et al., 2007). Therefore, it is a useful new method to simulate air mass evolution and variability, and its sensitivity to process parameters.

What processes drive the ocean heat transport?

The ocean contributes to regulating the Earth’s climate through its ability to transport heat from the equator to the poles. In this study we use long simulations of an ocean model to investigate whether the heat transport is carried primarily by wind-driven gyres or whether it is dominated by deep circulations associated with abyssal mixing and high latitude convection. The heat transport is computed as a function of temperature classes. In the Pacific and Indian ocean, the bulk of the heat transport is associated with wind-driven gyres confined to the thermocline. In the Atlantic, the thermocline gyres account for only 40% of the total heat transport. The remaining 60% is associated with a circulation reaching down to cold waters below the thermocline. Using a series of sensitivity experiments, we show that this deep heat transport is primarily set by the strength and patterns of surface winds and only secondarily by diabatic processes at high latitudes in the North Atlantic. Abyssal mixing below 2000 m has hardly any impact on ocean heat transport. A major implication is that the role of the ocean in regulating Earth’s climate strongly depends on how surface winds change across different climates in both hemispheres at low and high latitudes.

High-latitude ion transport and energetic explorer (HI-LITE): a mission to investigate ion outflow from the high-latitude ionosphere

The proposed HI-LITE Explorer will investigate the global ion outflow from the high-latitude ionosphere, its relationship to auroral features, and the consequences of this outflow on magnetospheric processes. The unique nature of the HI-LITE Explorer images will allow temporal and spatial features of the global ion outflow to be determined. The mission's scientific motivation comes from the fundamental role high-latitude ionospheric ions play in the dynamics of the solar wind driven magnetospheric-ionospheric system. These outflows are a major source of plasma for the magnetosphere and it is believed they play an important role in the triggering of substorms. In addition this paper describes the HI-LITE spacecraft and instruments.

Transport and distribution of lindane and simazine in a riverine environment: measurements in bed sediments and modelling

Aquatic sediments often remove hydrophobic contaminants from fresh waters. The subsequent distribution and concentration of contaminants in bed sediments determines their effect on benthic organisms and the risk of re-entry into the water and/or leaching to groundwater. This study examines the transport of simazine and lindane in aquatic bed sediments with the aim of understanding the processes that determine their depth distribution. Experiments in flume channels (water flow of 10 cm s(-1)) determined the persistence of the compounds in the absence of sediment with (a) de-ionised water and (b) a solution that had been in contact with river sediment. In further experiments with river bed sediments in light and dark conditions, measurements were made of the concentration of the compounds in the overlying water and the development of bacterial/algal biofilms and bioturbation activity. At the end of the experiments, concentrations in sediments and associated pore waters were determined in sections of the sediment at 1 mm resolution down to 5 mm and then at 10 mm resolution to 50 mm depth and these distributions analysed using a sorption-diffusion-degradation model. The fine resolution in the depth profile permitted the detection of a maximum in the concentration of the compounds in the pore water near the surface, whereas concentrations in the sediment increased to a maximum at the surface itself. Experimental distribution coefficients determined from the pore water and sediment concentrations indicated a gradient with depth that was partly explained by an increase in organic matter content and specific surface area of the solids near the interface. The modelling showed that degradation of lindane within the sediment was necessary to explain the concentration profiles, with the optimum agreement between the measured and theoretical profiles obtained with differential degradation in the oxic and anoxic zones. The compounds penetrated to a depth of 40-50 rum over a period of 42 days. (C) 2004 Society of Chemical Industry.

Mapping the spatial distribution of geomorphological processes in the Okstindan area of northern Norway, using Geomorphic Process Units as derived from remote sensing and ground survey

The delineation of Geomorphic Process Units (GPUs) aims to quantify past, current and future geomorphological processes and the sediment flux associated with them. Five GPUs have been identified for the Okstindan area of northern Norway and these were derived from the combination of Landsat satellite imagery (TM and ETM+) with stereo aerial photographs (used to construct a Digital Elevation Model) and ground survey. The Okstindan study area is sub-arctic and mountainous and is dominated by glacial and periglacial processes. The GPUs exclude the glacial system (some 37% of the study area) and hence they are focussed upon periglacial and colluvial processes. The identified GPUs are: 1. solifluction and rill erosion; 2. talus creep, slope wash and rill erosion; 3. accumulation of debris by rock and boulder fall; 4. rockwalls; and 5. stable ground with dissolved transport. The GPUs have been applied to a ‘test site’ within the study area in order to illustrate their potential for mapping the spatial distribution of geomorphological processes. The test site within the study area is a catchment which is representative of the range of geomorphological processes identified.

Atmospheric processes and observations

The central role of the atmosphere in abrupt climate change is proposed and discussed. This discussion is given in the context of the poleward transport of energy in the climate system and of climate variability and change. A number of examples based on observational and model data are used to illustrate the ideas.