Roseisalinus antarcticus gen. nov., sp nov., a novel aerobic bacteriochlorophyll a-producing alpha-proteobacterium isolated from hypersaline Ekho Lake, Antarctica

A Gram-negative, aerobic to microaerophilic rod was isolated from 10 m depths of the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica). The strain was oxidase- and catalase-positive, metabolized a variety of carboxylic acids and sugars and produced lipase. Cells had an absolute requirement for artificial sea water, which could not be replaced by NaCl. A large in vivo absorption band at 870 nm indicated production of bacteriochlorophyll a. The predominant fatty acids of this organism were 16:0 and 18:1omega7c, with 3-OH 10:0, 16:1omega7c and 18:0 in lower amounts. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The DNA G + C content was 67 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represents a member of the Roseobacter clade within the alpha-Proteobacteria. The organism showed no particular relationship to any members of this clade but clustered on the periphery of the genera Jannaschia, Octadecabacter and 'Marinosulfonomonas' and the species Ruegeria gelatinovorans. Distinct morphological, physiological and genotypic differences to these previously described taxa supported the description of a new genus and a novel species, for which the name Roseisalinus antarcticus gen. nov., sp. nov. is proposed. The type strain is EL-88(T) (= DSM 11466(T) = CECT 7023(T)).

Spectro-electrochemical and DFT studies of a planar Cu(II)–phenolate complex active in the aerobic oxidation of primary alcohols

A square-planar compound [Cu(pyrimol)Cl] (pyrimol = 4-methyl-2-N-(2-pyridylmethylene)aminophenolate) abbreviated as CuL–Cl) is described as a biomimetic model of the enzyme galactose oxidase (GOase). This copper(II) compound is capable of stoichiometric aerobic oxidation of activated primary alcohols in acetonitrile/water to the corresponding aldehydes. It can be obtained either from Hpyrimol (HL) or its reduced/hydrogenated form Hpyramol (4-methyl-2-N-(2-pyridylmethyl)aminophenol; H2L) readily converting to pyrimol (L-) on coordination to the copper(II) ion. Crystalline CuL–Cl and its bromide derivative exhibit a perfect square-planar geometry with Cu–O(phenolate) bond lengths of 1.944(2) and 1.938(2) Å. The cyclic voltammogram of CuL–Cl exhibits an irreversible anodic wave at +0.50 and +0.57 V versus ferrocene/ferrocenium (Fc/Fc+) in dry dichloromethane and acetonitrile, respectively, corresponding to oxidation of the phenolate ligand to the corresponding phenoxyl radical. In the strongly donating acetonitrile the oxidation path involves reversible solvent coordination at the Cu(II) centre. The presence of the dominant CuII–L. chromophore in the electrochemically and chemically oxidised species is evident from a new fairly intense electronic absorption at 400–480 nm ascribed to a several electronic transitions having a mixed pi-pi(L.) intraligand and Cu–Cl -> L. charge transfer character. The EPR signal of CuL–Cl disappears on oxidation due to strong intramolecular antiferromagnetic exchange coupling between the phenoxyl radical ligand (L.) and the copper(II) centre, giving rise to a singlet ground state (S = 0). The key step in the mechanism of the primary alcohol oxidation by CuL–Cl is probably the alpha-hydrogen abstraction from the equatorially bound alcoholate by the phenoxyl moiety in the oxidised pyrimol ligand, Cu–L., through a five-membered cyclic transition state.

Cropping systems, carbon sequestration and erosion in Brazil, a review

Soils represent a large carbon pool, approximately 1500 Gt, which is equivalent to almost three times the quantity stored in terrestrial biomass and twice the amount stored in the atmosphere. Any modification of land use or land management can induce variations in soil carbon stocks, even in agricultural systems that are perceived to be in a steady state. Tillage practices often induce soil aerobic conditions that are favourable to microbial activity and may lead to a degradation of soil structure. As a result, mineralisation of soil organic matter increases in the long term. The adoption of no-tillage systems and the maintenance of a permanent vegetation cover using Direct seeding Mulch-based Cropping system or DMC, may increase carbon levels in the topsoil. In Brazil, no-tillage practices (mainly DMC), were introduced approximately 30 years ago in the south in the Parana state, primarily as a means of reducing erosion. Subsequently, research has begun to study the management of the crop waste products and their effects on soil fertility, either in terms of phosphorus management, as a means of controlling soil acidity, or determining how manures can be applied in a more localised manner. The spread of no-till in Brazil has involved a large amount of extension work. The area under no-tillage is still increasing in the centre and north of the country and currently occupies ca. 20 million hectares, covering a diversity of environmental conditions, cropping systems and management practices. Most studies of Brazilian soils give rates of carbon storage in the top 40 cm of the soil of 0.4 to 1.7 t C ha(-1) per year, with the highest rates in the Cerrado region. However, caution must be taken when analysing DMC systems in terms of carbon sequestration. Comparisons should include changes in trace gas fluxes and should not be limited to a consideration of carbon storage in the soil alone if the full implications for global warming are to be assessed.

Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway

Nitrous oxide (N2O) emission from soils is a major contributor to the atmospheric loading of this potent greenhouse gas. It is thought that autotrophic ammonia oxidizing bacteria (AOB) are a significant source of soil-derived N2O and a denitrification pathway (i.e. reduction of NO2- to NO and N2O), so-called nitrifier denitrification, has been demonstrated as a N2O production mechanism in Nitrosomonas europaea. It is thought that Nitrosospira spp. are the dominant AOB in soil, but little information is available on their ability to produce N2O or on the existence of a nitrifier denitrification pathway in this lineage. This study aims to characterize N2O production and nitrifier denitrification in seven strains of AOB representative of clusters 0, 2 and 3 in the cultured Nitrosospira lineage. Nitrosomonas europaea ATCC 19718 and ATCC 25978 were analysed for comparison. The aerobically incubated test strains produced significant (P < 0.001) amounts of N2O and total N2O production rates ranged from 2.0 amol cell(-1) h(-1), in Nitrosospira tenuis strain NV12, to 58.0 amol cell(-1) h(-1), in N. europaea ATCC 19718. Nitrosomonas europaea ATCC 19718 was atypical in that it produced four times more N2O than the next highest producing strain. All AOB tested were able to carry out nitrifier denitrification under aerobic conditions, as determined by production of N-15-N2O from applied N-15-NO2-. Up to 13.5% of the N2O produced was derived from the exogenously applied N-15-NO2-. The results suggest that nitrifier denitrification could be a universal trait in the betaproteobacterial AOB and its potential ecological significance is discussed.

The Wheal Jane wetlands model for bioremediation of acid mine drainage

Acid mine drainage (AMD) is a widespread environmental problem associated with both working and abandoned mining operations. As part of an overall strategy to determine a long-term treatment option for AMD, a pilot passive treatment plant was constructed in 1994 at Wheal Jane Mine in Cornwall, UK. The plant consists of three separate systems, each containing aerobic reed beds, anaerobic cell and rock filters, and represents the largest European experimental facility of its kind. The systems only differ by the type of pretreatment utilised to increase the pH of the influent minewater (pH <4): lime dosed (LD), anoxic limestone drain (ALD) and lime free (LF), which receives no form of pretreatment. Historical data (1994-1997) indicate median Fe reduction between 55% and 92%, sulphate removal in the range of 3-38% and removal of target metals (cadmium, copper and zinc) below detection limits, depending on pretreatment and flow rates through the system. A new model to simulate the processes and dynamics of the wetlands systems is described, as well as the application of the model to experimental data collected at the pilot plant. The model is process based, and utilises reaction kinetic approaches based on experimental microbial techniques rather than an equilibrium approach to metal precipitation. The model is dynamic and utilises numerical integration routines to solve a set of differential equations that describe the behaviour of 20 variables over the 17 pilot plant cells on a daily basis. The model outputs at each cell boundary are evaluated and compared with the measured data, and the model is demonstrated to provide a good representation of the complex behaviour of the wetland system for a wide range of variables. (C) 2004 Elsevier B.V/ All rights reserved.

Bioremediation of acid mine drainage: an introduction to the Wheal Jane wetlands project

Acid mine drainage (AMD) is a widespread environmental problem associated with both working and abandoned mining operations. As part of an overall strategy to determine a long-term treatment option for AMD, a pilot passive treatment plant was constructed in 1994 at Wheat Jane Mine in Cornwall, UK. The plant consists of three separate systems; each containing aerobic reed beds, anaerobic cell and rock filters, and represents the largest European experimental facility of its kind. The systems only differ by the type of pre-treatment utilised to increase the pH of the influent minewater (pH<4): lime-dosed (LD), anoxic limestone drain (ALD) and lime free (LF), which receives no form of pre-treatment. The Wheal Jane pilot plant offered a unique facility and a major research project was established to evaluate the pilot plant and study in detail the biological mechanisms and the geochemical and physical processes that control passive treatment systems. The project has led to data, knowledge, models and design criteria for the future design, planning and sustainable management of passive treatment systems. A multidisciplinary team of scientists and managers from the U.K. universities, the Environment Agency and the Mining Industry has been put together to obtain the maximum advantage from the excellent facilities facility at Wheal Jane. (C) 2004 Elseaier B.V All rights reserved.

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

Biodegradation of polyethylene glycol (PEG) in three tropical soils using radio labelled PEG

Polyethylene glycol (PEG) may be added to forage based diets rich in tannins for ruminant feeding because it binds to tannins and thus prevent the formation of potentially indigestible tannin-protein complexes. The objective of this work was to determine the in vitro biodegradation (mineralization, i.e., complete breakdown of PEG to CO2) rate of PEG. C-14-Polyethylene glycol (C-14-PEG) was added to three different tropical soils (a sandy clay loam soil, SaCL; a sandy clay soil, SaC; and a sandy loam soil, SaL) and was incubated in Bartha flasks. Free PEG and PEG bound to tannins from a tannin rich local shrub were incubated under aerobic conditions for up to 70 days. The biodegradation assay monitored the (CO2)-C-14 evolved after degradation of the labelled PEG in the soils. After incubation, the amount of (CO2)-C-14 evolved from the C-14-PEG application was low. Higher PEG mineralization values were found for the soils with higher organic matter contents (20.1 and 18.6 g organic matter/kg for SaCL and SaC, respectively) than for the SaL soil (11.9 g organic matter/kg) (P < 0.05). The extent of mineralization of PEG after 70 days of incubation in the soil was significantly lower (P < 0.05) when it was added as bound to the browse tannin than in the free form (0.040 and 0.079, respectively). (c) 2005 Elsevier B.V. All rights reserved.

Effect of condensed tannins from tropical legumes on the activity of fibrolytic enzymes from the rumen fungus Neocallimastyx hurleyensis

A study was conducted to assess the effect of condensed tannins on the activity of fibrolytic enzymes from the anaerobic rumen fungus, Neocallimastix hurleyensis and a recombinant ferulic acid esterase (FAE) from the aerobic fungus Aspergillus niger. Condensed tannins were extracted from the tropical legumes Desmodium ovalifolium, Flemingia macrophylla, Leucaena leticocephala, Leucaena pallida, Calliandra calothyrsus and Clitoria fairchildiana and incubated in fungal enzyme mixtures or with the recombinant FAE. In most cases, the greatest reductions in enzyme activities were observed with tannins purified from D. ovalifolium and F macrophylla and the least with tannins from L leucocephala. Thus, whereas 40 mu g ml(-1) of condensed tannins from C. calothyrsus and L. leucocephala were needed to halve the activity of N. hurleyensis carboxymethylcellulase (CMCase), just 5.5 mu g ml(-1) of the same tannins were required to inhibit 50% of xylanase activity. The beta-D-glucosidase and beta-D-Xylosidase enzymes were less sensitive to tannin inhibition and concentrations greater than 100 mu g ml(-1) were required to reduce their activity by 50%. In other assays, the inhibitory effect of condensed tannins when added to incubation mixtures containing particulate substrates (the primary cell walls of E arundinacea) or when bound to these substrate was compared. Substrate-associated tannins were more effective in preventing fibrolytic activities than tannins added directly to incubations solutions. It was concluded that condensed tannins from tropical legumes can inhibit fibrolytic enzyme activities, although the extent of the effect was dependent on the tannin, the nature of its association with the substrate and the enzyme involved. (c) 2005 Elsevier Inc. All rights reserved.

Comparing rice production systems: A challenge for agronomic research and for the dissemination of knowledge-intensive farming practices

This article is a commentary on several research studies conducted on the prospects for aerobic rice production systems that aim at reducing the demand for irrigation water which in certain major rice producing areas of the world is becoming increasingly scarce. The research studies considered, as reported in published articles mainly under the aegis of the International Rice Research Institute (IRRI), have a narrow scope in that they test only 3 or 4 rice varieties under different soil moisture treatments obtained with controlled irrigation, but with other agronomic factors of production held as constant. Consequently, these studies do not permit an assessment of the interactions among agronomic factors that will be of critical significance to the performance of any production system. Varying the production factor of "water" will seriously affect also the levels of the other factors required to optimise the performance of a production system. The major weakness in the studies analysed in this article originates from not taking account of the interactions between experimental and non-experimental factors involved in the comparisons between different production systems. This applies to the experimental field design used for the research studies as well as to the subsequent statistical analyses of the results. The existence of such interactions is a serious complicating element that makes meaningful comparisons between different crop production systems difficult. Consequently, the data and conclusions drawn from such research readily become biased towards proposing standardised solutions for possible introduction to farmers through a linear technology transfer process. Yet, the variability and diversity encountered in the real-world farming environment demand more flexible solutions and approaches in the dissemination of knowledge-intensive production practices through "experiential learning" types of processes, such as those employed by farmer field schools. This article illustrates, based on expertise of the 'system of rice intensification' (SRI), that several cost-effective and environment-friendly agronomic solutions to reduce the demand for irrigation water, other than the asserted need for the introduction of new cultivars, are feasible. Further, these agronomic Solutions can offer immediate benefits of reduced water requirements and increased net returns that Would be readily accessible to a wide range of rice producers, particularly the resource poor smallholders. (C) 2009 Elsevier B.V. All rights reserved.

The effect of selective decontamination of the digestive tract on mortality in multiple trauma patients: a multicenter randomized controlled trial

Objective: Evaluation of selective decontamination of the digestive tract (SDD) on late mortality in ventilated trauma patients in an intensive care unit (ICU). Methods: A multicenter, randomized controlled trial was undertaken in 401 trauma patients with Hospital Trauma Index-Injury Severity Score of 16 or higher. Patients were randomized to control (n = 200) or SDD (n = 201), using polymyxin E, tobramycin, and amphotericin B in throat and gut throughout ICU treatment combined with cefotaxime for 4 days. Primary endpoint was late mortality excluding early death from hemorrhage or craniocerebral injury. Secondary endpoints were infection and organ dysfunction. Results: Mortality was 20.9% with SDD and 22.0% in controls. Overall late mortality was 15.3% (57/372) as 29 patients died from cerebral injury, 16 SDD and 13 control. The odds ratio (95% confidence intervals) of late mortality for SDD relative to control was 0.75 (0.40-1.37), corresponding to estimates of 13.4% SDD and 17.2% control. The overall infection rate was reduced in the test group (48.8% vs. 61.0%). SDD reduced lower airway infections (30.9% vs. 50.0%) and bloodstream infections due to aerobic Gram-negative bacilli (2.5% vs. 7.5%). No difference in organ dysfunction was found. Concluson: This study demonstrates that SDD significantly reduces infection in multiple trauma, although this RCT in 401 patients was underpowered to detect a mortality benefit.

EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E-coli O157 : H7

Escherichia coli possesses iron transporters specific for either Fe2+ or Fe3+. Although Fe2+ is far more soluble than Fe3+, it rapidly oxidizes aerobically at pH >= 7. Thus, FeoAB, the major Fe2+ transporter of E. coli, operates anaerobically. However, Fe2+ remains stable aerobically under acidic conditions, although a low-pH Fe2+ importer has not been previously identified. Here we show that ycdNOB (efeUOB) specifies the first such transporter. efeUOB is repressed at high pH by CpxAR, and is Fe2+-Fur repressed. EfeU is homologous to the high-affinity iron permease, Ftr1p, of Saccharomyces cerevisiae and other fungi. EfeO is periplasmic with a cupredoxin N-terminal domain; EfeB is also periplasmic and is haem peroxidase-like. All three Efe proteins are required for Efe function. The efeU gene of E. coli K-12 is cryptic due to a frameshift mutation - repair of the single-base-pair deletion generates a functional EfeUOB system. In contrast, the efeUOB operon of the enterohaemorrhagic strain, O157:1147, lacks any frameshift and is functional. A 'wild-type' K-12 strain bearing a functional EfeUOB displays a major growth advantage under aerobic, low-pH, low-iron conditions when a competing metal is provided. Fe-55 transport assays confirm the ferrous iron specificity of EfeUOB.

Studies on the effects of oxadiargyl on direct-seeded rice and Echinochloa crus-galli under drained and flooded conditions

Dose–response experiments were conducted in glasshouse pot experiments to investigate the selectivity of oxadiargyl, a recently introduced herbicide, in direct-seeded rice under both aerobic and anaerobic conditions. Crop sensitivity to oxadiargyl was comparatively greater for wet-seeded (anaerobic) than for dry-seeded rice (aerobic). Likewise, greater efficacy against Echinochloa crus-galli (L.) was also observed under anaerobic conditions. These results indicate greater activity of oxadiargyl under anaerobic conditions, but that application pre-sowing with subsequent flooding would reduce selectivity in wet-seeded rice. The results are discussed in relation to rice production in Mediterranean agriculture.