New methods for new questions about rhizosphere/plant root interactions

Plant and Soil - In this opinion paper we review recent methodological developments underpinning the study of roots, the rhizosphere and interactions affecting soil functions, and explore new...     

Synchrotron-Based Techniques Shed Light on Mechanisms of Plant Sensitivity and Tolerance to High Manganese in the Root Environment

Plant species differ in response to high available manganese (Mn), but the mechanisms of sensitivity and tolerance are poorly understood. In solution culture, greater than or equal to 30 µm Mn decreased the growth of soybean (Glycine max), but white lupin (Lupinus albus), narrow-leafed lupin (Lupin angustifolius), and sunflower (Helianthus annuus) grew well at 100 µm Mn. Differences in species’ tolerance to high Mn could not be explained simply by differences in root, stem, or leaf Mn status, being 8.6, 17.1, 6.8, and 9.5 mmol kg^–1 leaf fresh mass at 100 µm Mn. Furthermore, x-ray absorption near edge structure analyses identified the predominance of Mn(II), bound mostly to malate or citrate, in roots and stems of all four species. Rather, differences in tolerance were due to variations in Mn distribution and speciation within leaves. In Mn-sensitive soybean, in situ analysis of fresh leaves using x-ray fluorescence microscopy combined with x-ray absorption near edge structure showed high Mn in the veins, and manganite [Mn(III)] accumulated in necrotic lesions apparently through low Mn sequestration in vacuoles or other vesicles. In the two lupin species, most Mn accumulated in vacuoles as either soluble Mn(II) malate or citrate. In sunflower, Mn was sequestered as manganite at the base of nonglandular trichomes. Hence, tolerance to high Mn was ascribed to effective sinks for Mn in leaves, as Mn(II) within vacuoles or through oxidation of Mn(II) to Mn(III) in trichomes. These two mechanisms prevented Mn accumulation in the cytoplasm and apoplast, thereby ensuring tolerance to high Mn in the root environment.Manganese (Mn) is an essential element for plant growth, but its availability differs greatly in space and time, depending largely on the nature and amount of Mn minerals present and on the soil’s pH and redox potential. With an elaborate chemistry, Mn forms complexes with many organic and inorganic ligands. In soils, Mn has three common oxidation states, Mn(II), Mn(III), and Mn(IV), which form hydrated oxides of mixed valency; Mn is present also as numerous carbonates, silicates, sulfates, and phosphates (Lindsay, 1979). Cationic Mn²⁺ is the most common form readily absorbed by plant roots (Clarkson, 1988). The toxicity of Mn occurs in acid or waterlogged soils high in Mn minerals.Many plants have mechanisms to accommodate the large differences in Mn²⁺ in soils. At low available Mn, uptake is increased in some Poaceae by excretion of phytosiderophores of the mugineic acid family (Takahashi et al., 2003), with root phytase exudation also potentially important for acquisition of Mn when Mn availability is limited (George et al., 2014). Mechanisms in other plants include the ability of roots to decrease rhizosphere pH or excrete organic ligands (Neumann and Romheld, 2012; Lambers et al., 2015). However, the relative importance of the many complexes on Mn uptake remains unclear. Toxicity results from high Mn in leaf cell walls (Wissemeier et al., 1992; Wissemeier and Horst, 1992) and through adverse effects on symplastic proteins (Führs et al., 2008). Many plants have mechanisms that limit the adverse effects of high Mn²⁺ in soils, with numerous ligands involved in its translocation and that of other essential cations (Haydon and Cobbett, 2007). Edwards and Asher (1982) classified a range of crop and pasture species based on their ability to deal with high Mn as those that (1) limit Mn from entering the roots, (2) retain Mn in the roots, or (3) tolerate high Mn in the shoots. At the extreme are plants that hyperaccumulate more than 10,000 mg Mn kg^–1 on a dry mass (DM) basis in foliar tissues without metabolic damage (Fernando et al., 2013; van der Ent et al., 2013). Based on 15% DM of leaves, this equates to 12.1 mmol kg^–1 on a fresh mass (FM) basis. Celosia argentia, a species adapted to growth on Mn-contaminated mine tailings, accumulated more than 20,000 mg kg^–1 Mn in leaves (Liu et al., 2014). Tolerance of high Mn in shoots of some Mn hyperaccumulators has been found to occur through binding to ligands (such as malate or citrate) or sequestration in the vacuole (Fernando et al., 2010).Characteristic symptoms of Mn toxicity include chlorotic and distorted leaves with small necrotic lesions. These lesions have been shown in cowpea (Vigna unguiculata) to contain oxidized Mn and callose (Wissemeier et al., 1992), which forms as a reaction to high intracellular Ca (Kartusch, 2003). The necrotic lesions result mainly from oxidized phenolics (Wissemeier and Horst, 1992) and increased peroxidase activity in the apoplast (Horst et al., 1999). With a critical solution concentration for toxicity (10% growth reduction) of no more than 9 µm Mn, Edwards and Asher (1982) found that cotton (Gossypium hirsutum), bean (Phaseolus vulgaris), cowpea, and soybean (Glycine max) were the most sensitive species of 13 crop and pasture plants grown for 18 to 31 d at constant Mn in solution culture. By contrast, the critical concentration for sunflower (Helianthus annuus) was 7 times higher at 65 µm Mn. Sunflower was the first species found to tolerate high Mn through its sequestration in the trichomes on stems, petioles, and leaves (Blamey et al., 1986). The suspected accumulation of Mn was confirmed using wavelength dispersive x-ray spectroscopy with darkening inferred as due to insoluble higher oxides of Mn. Similarly, high Mn results in darkened trichomes of cucumber (Cucumis sativus) leaves due to oxidized Mn, as shown by the colorimetric benzidine test (Horiguchi, 1987). Watermelon (Citrullus lanatus; Elamin and Wilcox, 1986b), but not muskmelon (Citrullus melo; Elamin and Wilcox, 1986a), grown at high Mn also develops small dark spots around the leaf trichomes. Other species that sequester Mn in the trichomes include common nettle (Urtica dioica; Hughes and Williams, 1988) and Alyssum murale, a Ni hyperaccumulator (Broadhurst et al., 2009; McNear and Küpper, 2014). Thus, some plants in four families, Asteraceae, Cucurbitaceae, Urticaceae, and Brassicaceae, tolerate high Mn in shoots through Mn sequestration in or around the trichomes. The mechanisms may differ, however, because the high Mn present during development of common nettle stinging hairs decreases as plants mature (Hughes and Williams, 1988).Recently developed techniques, including those based on synchrotron radiation, allow investigations of the distribution and speciation of Mn in planta, with most research to date focused on Mn hyperaccumulators (Fernando et al., 2013). For example, Fernando et al. (2010) used x-ray absorption near-edge spectroscopy (XANES) to confirm the widely accepted view that Mn(II) predominates in seven Mn hyperaccumulators. Synchrotron-based x-ray fluorescence microspectroscopy (µ-XRF) was used by McNear and Küpper (2014) to show that the basal region of trichomes of A. murale plants grown at no more than 10 µm Mn contained Mn(II) complexed with phosphate. At 50 µm Mn in solution, however, the increased amount of Mn that had accumulated around the trichomes was present as Mn(III). Few studies, however, have used synchrotron-based techniques to investigate the mechanisms of Mn toxicity and tolerance in agronomic species despite their importance for food production in regions where soils are acidic or intermittently waterlogged. One study on cowpea, with a critical toxicity concentration of only 2 µm Mn (Edwards and Asher, 1982), has shown an accumulation of Mn-citrate in the root cap and associated mucigel within 5 min of exposure to 150 µm Mn (Kopittke et al., 2013).This study aimed to determine the distribution and speciation of Mn in fresh roots, stems, and leaves of four crop species, soybean, white lupin (Lupinus albus), narrow-leafed lupin (Lupinus angustifolius), and sunflower, which differ in tolerance to high Mn. It was hypothesized that Mn distribution and speciation would differ between Mn-sensitive soybean and the three other species. Furthermore, we considered it likely that the Mn tolerance mechanism of sunflower would differ from those of the two lupin species, which do not have darkened trichomes when grown at high Mn.     

Differential retrotranslocation of mitochondrial Bax and Bak

The Bcl-2 proteins Bax and Bak can permeabilize the outer mitochondrial membrane and commit cells to apoptosis. Pro-survival Bcl-2 proteins control Bax by constant retrotranslocation into the cytosol of healthy cells. The stabilization of cytosolic Bax raises the question whether the functionally redundant but largely mitochondrial Bak shares this level of regulation. Here we report that Bak is retrotranslocated from the mitochondria by pro-survival Bcl-2 proteins. Bak is present in the cytosol of human cells and tissues, but low shuttling rates cause predominant mitochondrial Bak localization. Interchanging the membrane anchors of Bax and Bak reverses their subcellular localization compared to the wild-type proteins. Strikingly, the reduction of Bax shuttling to the level of Bak retrotranslocation results in full Bax toxicity even in absence of apoptosis induction. Thus, fast Bax retrotranslocation is required to protect cells from commitment to programmed death.     

Tight coupling of primary production and marine mammal reproduction in the Southern Ocean

Polynyas are areas of open water surrounded by sea ice and are important sources of primary production in high-latitude marine ecosystems. The magnitude of annual primary production in polynyas is controlled by the amount of exposure to solar radiation and sensitivity to changes in sea-ice extent. The degree of coupling between primary production and production by upper trophic-level consumers in these environments is not well understood, which prevents reliable predictions about population trajectories for species at higher trophic levels under potential future climate scenarios. In this study, we find a strong, positive relationship between annual primary production in an Antarctic polynya and pup production by ice-dependent Weddell seals. The timing of the relationship suggests reproductive effort increases to take advantage of high primary production occurring in the months after the birth pulse. Though the proximate causal mechanism is unknown, our results indicate tight coupling between organisms at disparate trophic levels on a short timescale, deepen our understanding of marine ecosystem processes, and raise interesting questions about why such coupling exists and what implications it has for understanding high-latitude ecosystems.     

Ppm1E is an in cellulo AMP-activated protein kinase phosphatase

Activation of 5′-AMP-activated protein kinase (AMPK) is believed to be the mechanism by which the pharmaceuticals, metformin and phenformin, exert their beneficial effects for treatment of type 2 diabetes. These biguanide drugs elevate 5′-AMP, which allosterically activates AMPK and promotes phosphorylation on Thr172 of AMPK catalytic α subunits. Although kinases phosphorylating this site have been identified, phosphatases that dephosphorylate it are unknown. The aim of this study is to identify protein phosphatase(s) that dephosphorylate AMPKα-Thr172 within cells. Our initial data indicated that members of the protein phosphatase ce:sup>/ce:sup>/Mn²⁺-dependent (PPM) family and not those of the PPP family of protein serine/threonine phosphatases may be directly or indirectly inhibited by phenformin. Using antibodies raised to individual Ppm phosphatases that facilitated the assessment of their activities, phenformin stimulation of cells was found to decrease the ce:sup>/ce:sup>/Mn²⁺-dependent protein serine/threonine phosphatase activity of Ppm1E and Ppm1F, but not that attributable to other PPM family members, including Ppm1A/PP2Cα. Depletion of Ppm1E, but not Ppm1A, using lentiviral-mediated stable gene silencing, increased AMPKα-Thr172 phosphorylation approximately three fold in HEK293 cells. In addition, incubation of cells with low concentrations of phenformin and depletion of Ppm1E increased AMPK phosphorylation synergistically. Ppm1E and the closely related Ppm1F interact weakly with AMPK and assays with lysates of cells stably depleted of Ppm1F suggests that this phosphatase contributes to dephosphorylation of AMPK. The data indicate that Ppm1E and probably PpM1F are in cellulo AMPK phosphatases and that Ppm1E is a potential anti-diabetic drug target.     

Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages

Whole genome duplication ~70 million years ago provided raw material for Poaceae (grass) diversification. Comparison of rice (Oryza sativa), sorghum (Sorghum bicolor), maize (Zea mays), and Brachypodium distachyon genomes revealed that one paleo-duplicated chromosome pair has experienced very different evolution than all the others. For tens of millions of years, the two chromosomes have experienced illegitimate recombination that has been temporally restricted in a stepwise manner, producing structural stratification in the chromosomes. These strata formed independently in different grass lineages, with their similarities (low sequence divergence between paleo-duplicated genes) preserved in parallel for millions of years since the divergence of these lineages. The pericentromeric region of this homeologous chromosome pair accounts for two-thirds of the gene content differences between the modern chromosomes. Both intriguing and perplexing is a distal chromosomal region with the greatest DNA similarity between surviving duplicated genes but also with the highest concentration of lineage-specific gene pairs found anywhere in these genomes and with a significantly elevated gene evolutionary rate. Intragenomic similarity near this chromosomal terminus may be important in hom(e)ologous chromosome pairing. Chromosome structural stratification, together with enrichment of autoimmune response-related (nucleotide binding site-leucine-rich repeat) genes and accelerated DNA rearrangement and gene loss, confer a striking resemblance of this grass chromosome pair to the sex chromosomes of other taxa.     

Antibiotic dosing in the 'at risk' critically ill patient: Linking pathophysiology with pharmacokinetics/pharmacodynamics in sepsis and trauma patients

Background

Critical illness, mediated by trauma or sepsis, can lead to physiological changes that alter the pharmacokinetics of antibiotics and may result in sub-therapeutic concentrations at the sites of infection. The first aim of this project is to identify the clinical characteristics of critically ill patients with significant trauma that have been recently admitted to ICU that may predict the dosing requirements for the antibiotic, cefazolin. The second aim of this is to identify the clinical characteristics of critically ill patients with sepsis that may predict the dosing requirements for the combination antibiotic, piperacillin-tazobactam.

Methods/Design

This is an observational pharmacokinetic study of patients with trauma (cefazolin) or with sepsis (piperacillin-tazobactam). Participants will have samples from blood and urine, collected at different intervals. Patients will also have a microdialysis catheter inserted into subcutaneous tissue to measure interstitial fluid penetration of the antibiotic. Participants will be administered sinistrin, indocyanine green and sodium bromide as well as have cardiac output monitoring performed and tetrapolar bioimpedance to determine physiological changes resulting from pathology. Analysis of samples will be performed using validated liquid chromatography tandem mass-spectrometry. Pharmacokinetic analysis will be performed using non-linear mixed effects modeling to determine individual and population pharmacokinetic parameters of antibiotics.

Discussion

The study will describe cefazolin and piperacillin-tazobactam concentrations in plasma and the interstitial fluid of tissues in trauma and sepsis patients respectively. The results of this study will guide clinicians to effectively dose these antibiotics in order to maximize the concentration of antibiotics in the interstitial fluid of tissues.     

The relation between cartilage biomarkers (C2C,C1,2C,CS846, and CPII) and the long-term outcome of rheumatoid arthritis patients within the CAMERA trial

Introduction  

The aim of this study was to investigate whether serum biomarker levels of C2C, C1,2C, CS846, and CPII can predict the long-term course of disease activity and radiographic progression early in the disease course of rheumatoid arthritis (RA).     

Estimating metabolic heat loss in birds and mammals by combining infrared thermography with biophysical modelling

Infrared thermography (IRT) is a technique that determines surface temperature based on physical laws of radiative transfer. Thermal imaging cameras have been used since the 1960s to determine the surface temperature patterns of a wide range of birds and mammals and how species regulate their surface temperature in response to different environmental conditions. As a large proportion of metabolic energy is transferred from the body to the environment as heat, biophysical models have been formulated to determine metabolic heat loss. These models are based on heat transfer equations for radiation, convection, conduction and evaporation and therefore surface temperature recorded by IRT can be used to calculate heat loss from different body regions. This approach has successfully demonstrated that in birds and mammals heat loss is regulated from poorly insulated regions of the body which are seen to be thermal windows for the dissipation of body heat. Rather than absolute measurement of metabolic heat loss, IRT and biophysical models have been most useful in estimating the relative heat loss from different body regions. Further calibration studies will improve the accuracy of models but the strength of this approach is that it is a non-invasive method of measuring the relative energy cost of an animal in response to different environments, behaviours and physiological states. It is likely that the increasing availability and portability of thermal imaging systems will lead to many new insights into the thermal physiology of endotherms.