Effects of drought stress memory on the accumulation of stress-protective compounds in naturally grown pine and spruce

Forest trees are subjected to multiple stressors during their long lifetime and therefore require effective and finely regulated stress-protective systems. Stressors can induce protective systems either directly or with the involvement of stress memory mechanisms. Stress memory has only begun to be uncovered in model plants and is unexplored in coniferous species. Therefore, we studied the possible role of stress memory in the regulation of the accumulation of stress-protective compounds (heat shock proteins, dehydrins, proline) in the needles of naturally grown Scots pine and Norway spruce trees subjected to the subsequent action of long-term (multiyear) and short-term (seasonal) water shortages. Although the water deficit was relatively mild, it significantly influenced the pattern of expression of stress memory-related heat shock factor (HSF) and SWI/SNF genes, indicating the formation of stress memory in both species. In spruce, dehydrin accumulation was increased by water shortage in a manner compatible with Type II stress memory. The accumulation of HSP40 in spruce needles was positively influenced by long-term water shortage, but this increase was unlikely to be of biological importance due to the concomitant decrease in HSP70, HSP90 and HSP101 accumulation. Finally, proline accumulation was negatively influenced by short-term water deficit in spruce. In pine, no one protective compound accumulated in response to water stress. Taken together, the results indicate that the accumulation of stress-protective compounds was generally independent of stress memory effects both in pine and in spruce.

Abscisic Acid and Cytokinins Are Not Involved in the Regulation of Stomatal Conductance of Scots Pine Saplings during Post-Drought Recovery

Delayed or incomplete recovery of gas exchange after water stress relief limits assimilation in the post-drought period and can thus negatively affect the processes of post-drought recovery. Abscisic acid (ABA) accumulation and antagonistic action between ABA and cytokinins (CKs) play an important role in regulation of stomatal conductance under water deficit. Specifically, in pine species, sustained ABA accumulation is thought to be the main cause of delayed post-drought gas exchange recovery, although the role of CKs is not yet known. Therefore, we aimed to study the effects of ABA and CKs on recovery of stomatal conductance in greenhouse-grown 3-year-old Scots pine saplings recovering from water stress. We analysed both changes in endogenous ABA and CK contents and the effects of treatment with exogenous CK on stomatal conductance. Drought stress suppressed stomatal conductance, and post-drought stomatal conductance remained suppressed for 2 weeks after plant rewatering. ABA accumulated during water stress, but ABA levels decreased rapidly after rewatering. Additionally, trans-zeatin/ABA and isopentenyladenine/ABA ratios, which were decreased in water-stressed plants, recovered rapidly in rewatered plants. Spraying plants with 6-benzylaminopurine (0.1–100 µM) did not influence recovery of either stomatal conductance or needle water status. It can be concluded that the delayed recovery of stomatal conductance in Scots pine needles was not due to sustained ABA accumulation or a sustained decrease in the CK/ABA ratio, and CK supplementation was unable to overcome this delayed recovery.

Manganese Deficiency Suppresses Growth and Photosynthetic Processes but Causes an Increase in the Expression of Photosynthetic Genes in Scots Pine Seedlings

Manganese deficiency is a serious plant nutritional disorder, resulting in the loss of crop productivity in many parts of the world. Despite the progress made in the study of angiosperms, the demand for Mn in gymnosperms and the physiological responses to Mn deficiency remain unexplored. We studied the influence of Mn deficiency for 24 weeks on Pinus sylvestris L. seedling growth, ion homeostasis, pigment contents, lipid peroxidation, chlorophyll fluorescence indices and the transcript levels of photosynthetic genes and genes involved in chlorophyll biosynthesis. It was shown that Mn-deficient plants demonstrated suppressed growth when the Mn content in the needles decreased below 0.34 µmol/g DW. The contents of photosynthetic pigments decreased when the Mn content in the needles reached 0.10 µmol/g DW. Mn deficiency per se did not lead to a decrease in the nutrient content in the organs of seedlings. Photoinhibition of PSII was observed in Mn-deficient plants, although this was not accompanied by the development of oxidative stress. Mn-deficient plants had an increased transcript abundance of genes (psbO, psbP, psbQ, psbA and psbC), encoding proteins directly associated with the Mn cluster also as other proteins involved in photosynthesis, whose activities do not depend on Mn directly. Furthermore, the transcript levels of the genes encoding the large subunit of Rubisco, light-dependent NADPH-protochlorophyllide oxidoreductase and subunits of light-independent protochlorophyllide reductase were also increased in Mn-deficient plants.

Stem notching decreases stem hydraulic conductance but does not influence drought impacts and post-drought recovery in Scots pine and Norway spruce

The tight connection between the deterioration of xylem function and plant mortality under drought is well recognized. However, a lack of mechanistic understanding of how substantial conductivity loss influences plant performance under drought and during post-drought recovery hinders our ability to model tree responses to drought stress. We artificially induced a loss of 50% of xylem conducting area in Scots pine and Norway spruce saplings by stem notching and investigated plant performance under drought and during post-drought recovery. Plant mortality, xylem hydraulic conductivity, leaf water status and stomatal conductance were measured. We observed no preferential mortality of top plant parts (above the notches) compared to basal plant parts (below the notches), and no consistent trend in hydraulic conductivity loss was observed between top and basal parts of dying plants. Stem hydraulic conductivity, water status of the needles and stomatal conductance changed similarly between the top and basal parts during drought and post-drought recovery, which indicated the substantial hydraulic overcapacity of the stems. The recovery of stomatal conductance demonstrated prominent hysteresis due to non-hydraulic stomatal limitations. The results obtained are highly important for modelling the influence of plant hydraulic impairment on plant performance under drought and during post-drought recovery.

Mineral Nutrition of Naturally Growing Scots Pine and Norway Spruce under Limited Water Supply

The deterioration of plant mineral nutrition during drought is a significant factor in the negative influence of drought on plant performance. We aimed to study the effects of seasonal and multiyear water shortages on nutrient supply and demand in Scots pine and Norway spruce. We studied pine and spruce trees naturally grown in the Bryansk region (Russia). The dynamics of several nutrients (K, Ca, Mg, P, Fe, Mn, Zn, and Ca) in wood, needles, and bark of current-year twigs and the dynamics of the available pools of these elements at different soil depths were analysed. To assess the physiological consequences of changes in element concentrations, lipid peroxidation products and photosynthetic pigments were measured in the needles. Water shortage increased the wood concentrations of all elements except for Mn. In pine, this increase was mainly due to seasonal water deficit, whereas in spruce, multiyear differences in water supply were more important. This increased availability of nutrients was not observed in soil-based analyses. In needles, quite similar patterns of changes were found between species, with Mg increasing almost twofold and Fe and Mn decreasing under water shortage, whereas the remainder of the elements did not change much under differing water supplies. Neither the concentrations of photosynthetic pigments nor the contents of lipid peroxidation products correlated with element dynamics in needles. In summary, water shortage increased the availability of all elements except Mn for the plant; however, needle element contents were regulated independently of element availability for plants.

[Epithelial-stromal interactions in pancreatic adenocarcinoma: the role of stroma in disease progression]

Pancreatic ductal adenocarcinoma (PDAC) is the most common and difficult to treat form of pancreas cancer. PDAC and other solid cancers contain both tumor cells and normal connective tissue cells called stromal cells, which are responsible for the excess production of extracellular matrix. It is known that in more than 90% of PDAC tumors and in many other types of cancer, mutations of the KRAS gene are observed, the reciprocal signaling of which has been shown between tumor and stromal cells in vitro. Pancreatic stromal stellate cells are considered precursors of activated or tumor-associated fibroblasts (CAFs), which are an increasing population of cells that proliferate in situ or are recruited into the tumor. CAFs are a heterogeneous population of stromal fibroblasts with different molecular profiles that change during tumorigenesis. Both immunosuppressive and immunosuppressive subsets of CAFs can coexist in the stroma of a single tumor. Based on the heterogeneity of the intertumor stroma, attempts are being made to classify PDAC and predict the course of the disease.

Quantitative analysis of differential dehydrin regulation in pine and spruce seedlings under water deficit

Dehydrins are well-known components of plant responses to different stresses that cause dehydration, including drought, freezing, salinity, etc. In conifers, the dehydrin gene family is very large, implying that the members of this family have important physiological functions in conifer stress tolerance. However, dehydrin gene expression displays a wide range of responses to stress, from thousand-fold increased expression to decreased expression, and it is generally unknown how regulatory systems are connected at the mRNA and protein levels. Therefore, we studied these aspects of dehydrin regulation in Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) H. Karst) seedlings under polyethylene glycol 6000-induced osmotic stress ranging from relatively low (culture medium water potential of -0.15 MPa) to very high (-1.0 MPa) intensities. In pine, the major dehydrin protein was Dhn1 in both the roots and needles, and in spruce, two isoforms of the Dhn4 protein were the major dehydrins; both of these proteins are AESK-type dehydrins. The genes encoding these major proteins were highly expressed even under control conditions; surprisingly, we also observed several highly expressed dehydrin genes that were not abundantly translated. Under osmotic stress, the most prominent expression changes were observed for the dehydrin genes with low basal expression levels, whereas highly expressed genes generally demonstrated rather modest changes in expression. We report proposed constitutive physiological functions of the AESK-type dehydrins in Pinaceae plants.

Phytotoxicity of short-term exposure to excess zinc or copper in Scots pine seedlings in relation to growth, water status, nutrient balance, and antioxidative activity

The toxic effects of heavy metals pose a significant threat to the productivity and stability of forest ecosystems. Changes in the agrochemical properties of polluted forest soils due to global climate changes can increase the bioavailability of previously immobilized heavy metals. To test this hypothesis, we studied the effects of short-term shock exposure to ZnSO₄ (50, 150, 300 μM) or CuSO₄ (2.5, 5, 10 μM) in hydroculture on 4- to 6-week-old seedlings of Scots pine (Pinus sylvestris L.) with well-developed root systems. The effects of the excess heavy metals on mineral nutrients and the functioning of low-molecular-weight antioxidants and glutathione in protecting plants from oxidative damage were studied. Even short-term exposure to exogenous metals led to their rapid accumulation in the root system and their subsequent transport to aboveground organs. An increase in the 4-hydroxyalkenals content in seedling needles exposed to excess Cu led to an increase in the content of proanthocyanidins and catechins, which act as scavengers of reactive oxygen species. The impact of both metals led to the rapid development of mineral nutrient imbalances in the seedlings, which were most pronounced in the presence of excess Zn. Exposure to excess Zn led to a disruption in the translocation of Fe and a decrease in the Fe content in the needles. The most dramatic consequence of Zn exposure was the development of Mn deficiency in the roots, which was the likely cause of the inhibition of phenolic compound synthesis. A deficiency in phenolic compounds can have serious environmental consequences for pine populations that are at risk of contamination by Zn and Cu salts.

Profiles of endogenous phytohormones and expression of some hormone-related genes in Scots pine and Norway spruce seedlings under water deficit

Different plant hormones are involved in plant adaptation to water deficit. In comparison to angiosperms, little is known about the impact of drought on the pool of phytohormones in gymnosperms. Therefore, we studied the effect of polyethylene glycol-induced water deficit on the changes in content of different phytohormones in Scots pine and Norway spruce seedlings, which are known for their different strategies of adaptation to water deficit. The following hormone classes were analysed: cytokinins, auxins, jasmonates, salicylic and benzoic acids, and 1-aminocyclopropane-1-carboxylic acid (an ethylene precursor). No consistent reaction to water stress was observed for the content of well-known stress-related hormones - salicylic acid and jasmonates. In contrast, drought induced a dose-dependent accumulation of cytokinins in pine needles, with less profound changes in spruce needles. The most prominent changes were observed for 1-aminocyclopropane-1-carboxylic acid content, which increased several-fold in spruce roots and pine needles under water deficit. Water-deficit-induced changes in the contents of cytokinins and 1-aminocyclopropane-1-carboxylic acid were accompanied by the differential regulation of genes involved in the metabolism of these hormones. Possible links between changes in hormone pools and the adaptation of seedlings to water deficit are discussed.

Comparative analysis of abscisic acid levels and expression of abscisic acid-related genes in Scots pine and Norway spruce seedlings under water deficit

Abscisic acid (ABA) is one of the main participants in the regulation of plant responses to water deficiency. Knowledge of the ABA signal transduction pathways in gymnosperms is rather limited, especially in comparison with those in angiosperms. Seedlings of Scots pine and Norway spruce are known for their contrasting behaviour strategies under water deficit. To characterize the possible role of ABA in these differences, ABA dynamics were investigated under conditions of water deficit in seedlings of these two species. The content of ABA and its catabolites was followed in the roots and needles of seedlings of Pinus sylvestris and Picea abies under conditions of polyethylene glycol (PEG)-induced water deficiency (-0.15 and -0.5 MPa) for 10 days. The expression of the main genes for ABA-biosynthetic enzymes was also analysed. ABA showed more pronounced stress-dependent dynamics in pine roots than in spruce roots, whereas in needles, the response was greater for spruce than pine. The ABA increase during drought was mainly due to de novo synthesis and the shift in the balance between ABA synthesis and catabolism towards synthesis. The ABA-glucosyl ester did not serve as a reserve for the release of free ABA under water deficiency. The expression levels of the main ABA biosynthetic genes showed a weak or no correlation with changes in ABA content under water stress, i.e., the ABA content in the seedlings of both species was not directly linked to the transcript levels of the main ABA biosynthetic genes. Less-pronounced stress-induced changes in ABA in pine needles than in spruce needles may be related to pine seedlings having a less conservative strategy of growth and maintenance of water balance under water deficit.

Impact of weak water deficit on growth, photosynthetic primary processes and storage processes in pine and spruce seedlings

We investigated the influence of 40 days of drought on growth, storage processes and primary photosynthetic processes in 3-month-old Scots pine and Norway spruce seedlings growing in perlite culture. Water stress significantly affected seedling water status, whereas absolute dry biomass growth was not substantially influenced. Water stress induced an increase in non-structural carbohydrate content (sugars, sugar alcohols, starch) in the aboveground part of pine seedlings in contrast to spruce seedlings. Due to the relatively low content of sugars and sugar alcohols in seedling organs, their expected contribution to osmotic potential changes was quite low. In contrast to biomass accumulation and storage, photosynthetic primary processes were substantially influenced by water shortage. In spruce seedlings, PSII was more sensitive to water stress than PSI. In particular, electron transport in PSI was stable under water stress despite the substantial decrease of electron transport in PSII. The increase in thermal energy dissipation due to enhancement of non-photochemical quenching (NPQ) was evident in both species under water stress. Simultaneously, the yields of non-regulated energy dissipation in PSII were decreased in pine seedlings under drought. A relationship between growth, photosynthetic activities and storage processes is analysed under weak water deficit.

Long-term impact of cement plant emissions on the elemental composition of both soils and pine stands and on the formation of Scots pine seeds

We investigated the long-term impact of the largest Russian cement plant on mesopodzol sandy soils and Scots pine stands. We determined the distributions of the total and available pools of Ca, Mg, K, Na, Mn, Fe, Zn, Ni, Cu, Pb and Cd in the soil profile to a depth of 60 cm (illuvial horizon) as well as the accumulation patterns of these elements in the vegetative and generative organs of Scots pine trees. High Ca accumulation in the impact zone soils was a result of CaO emissions by a cement plant. Also, CaO became the main cause of soil profile alkalization due to neutralization of soil acids and formation of calcium hydroxide or carbonates. Alkalization immobilized substantial amounts of Fe, Mn, Zn and Ni in the soil, reducing their availability. The most prominent effect of long-term cement production was a prominent Mn deficiency in vegetative and generative Scots pine organs due to the exhaustion of the available Mn pool in the illuvial horizon. The miniaturization of cones, a decrease in seed yield and a reduction in seed germinability were observed in the emission impact zones. Pretreatment of Mn-deficient seeds with manganese eliminated Mn deficiency but did not increase seed germination.

The effect of energy-dependent electron scattering on thermoelectric transport in novel topological semimetal CoSi

Cobalt monosilicide and its solid solutions with Fe or Ni crystallize in B20 cubic noncentrosymmetric structure. These compounds have long been known as promising thermoelectric materials. Recently it was revealed, that they also have unconventional electronic topology. This renewed interest to the investigation of their transport properties. In order to improve theoretical description of thermoelectric transport in these compounds, we take into account electron scattering beyond commonly used constant relaxation time approximation. Using first principle calculations, we investigate the scattering of charge carriers by phonons and point defects. The dependence of the scattering rate on the energy correlates with that for the total density of states. This implies that in this material not only the intraband, but also the interband scattering is important, especially for bands with low density of states. The Seebeck coefficient and the electrical resistivity of CoSi and of dilute solid solutions Co_1-x M _x Si (M  =  Fe or Ni, x  <  0.1) are calculated as a function of temperature and the alloy composition. We show that the account of strong energy dependence of relaxation time is important for the description of experimentally observed rapid increase of the resistivity and qualitative change of its temperature dependence with the substitution of cobalt for iron, as well as for the description of the magnitude of the Seebeck coefficient, its temperature and composition dependence.

Virulent Epidemic Pneumonia in Sheep Caused by the Human Pathogen Acinetobacter baumannii

The human pathogen Acinetobacter baumannii has emerged as a frequent cause of hospital-acquired infections, but infection of animals has rarely been observed. Here we analyzed an outbreak of epidemic pneumonia killing hundreds of sheep on a farm in Pakistan and identified A. baumannii as the infecting agent. A pure culture of strain AbPK1 isolated from lungs of sick animals was inoculated into healthy sheep, which subsequently developed similar disease symptoms. Bacteria re-isolated from the infected animals were shown to be identical to the inoculum, fulfilling Koch’s postulates. Comparison of the AbPK1 genome against 2283 A. baumannii genomes from the NCBI database revealed that AbPK1 carries genes for unusual surface structures, including a unique composition of iron acquisition genes, genes for O-antigen synthesis and sialic acid-specific acetylases of cell-surface carbohydrates that could enable immune evasion. Several of these unusual and otherwise rarely present genes were also identified in genomes of phylogenetically unrelated A. baumannii isolates from combat-wounded US military from Afghanistan indicating a common gene pool in this geographical region. Based on core genome MLST this virulent isolate represents a newly emerging lineage of Global Clone 2, suggesting a human source for this disease outbreak. The observed epidemic, direct transmission from sheep to sheep, which is highly unusual for A. baumannii, has important consequences for human and animal health. First, direct animal-to-animal transmission facilitates fast spread of pathogen and disease in the flock. Second, it may establish a stable ecological niche and subsequent spread in a new host. And third, it constitutes a serious risk of transmission of this hyper-virulent clone from sheep back to humans, which may result in emergence of contagious disease amongst humans.

Band structure and unconventional electronic topology of CoSi

Semimetals with certain crystal symmetries may possess unusual electronic structure topology, distinct from that of the conventional Weyl and Dirac semimetals. Characteristic property of these materials is the existence of band-touching points with multiple (higher than two-fold) degeneracy and nonzero Chern number. CoSi is a representative of this group of materials exhibiting the so-called 'new fermions'. We report on an ab initio calculation of the electronic structure of CoSi using density functional methods, taking into account the spin-orbit interactions. The linearized [Formula: see text] Hamiltonian, describing the anisotropic electronic structure of CoSi near the Γ point is derived. The topological features of band-touching nodes with four- and six-fold degeneracy located at the Γ and R points in the first Brillouin zone are analysed using the linearized Hamiltonians and first principle calculations. In particular, we show, using the non-Abelian Berry curvature, that these band-touching points carry topological charges of [Formula: see text], which change signs at certain values of parameters of the Hamiltonians. We describe the resulting Fermi arc surface states and their spin texture. We also discuss the influence of many body [Formula: see text] corrections on the electronic band structure and the topological properties of CoSi.

Impact of drought stress induced by polyethylene glycol on growth, water relations and cell viability of Norway spruce seedlings

We investigated physiological responses of 7-week-old Norway spruce seedlings to water deficits of different intensities. Hydroponically grown seedlings were subjected to mild (-0.15 MPa), strong (-0.5 and -1.0 MPa) and extreme (-1.5 MPa) water deficit induced by polyethylene glycol 6000, and their growth parameters, water status and physiological activity were analyzed. Seedlings effectively restricted water loss under drought, and even under extreme water deficit, shoot relative water content did not fall below 85%. Water stress induced substantial decreases in the osmotic potentials of root and needle cell sap, up to 0.3-0.4 MPa under extreme water deficit, though this did not result from water loss or accumulation of K⁺ and Na⁺ ions. Seedling growth was very susceptible to water stress because of poor capacity for cell wall adjustment. Water stress injured seedling roots, as evidenced by the loss of root cell physiological activity estimated by the ability to hydrolyse fluorescein diacetate and by increased root calcium content up to 8-10-fold under extreme water stress. At the same time, root hair growth was enhanced, especially under mild water deficit, which increased the root water-absorbing capacity. In summary, seedlings of Norway spruce were characterized by high susceptibility to water stress and concurrently by pronounced ability to maintain water status. These characteristics are fully consistent with spruce confinement to moist habitats.

Identification and taxonomic characterization of Bordetella pseudohinzii sp. nov. isolated from laboratory-raised mice

Bordetella hinzii is known to cause respiratory disease in poultry and has been associated with a variety of infections in immunocompromised humans. In addition, there are several reports of B. hinzii infections in laboratory-raised mice. Here we sequenced and analysed the complete genome sequences of multiple B. hinzii-like isolates, obtained from vendor-supplied C57BL/6 mice in animal research facilities on different continents, and we determined their taxonomic relationship to other Bordetella species. The whole-genome based and 16S rRNA gene based phylogenies each identified two separate clades in B. hinzii, one was composed of strains isolated from poultry, humans and a rabbit whereas the other clade was restricted to isolates from mice. Distinctly different estimated DNA–DNA hybridization values, average nucleotide identity scores, gene content, metabolic profiles and host specificity all provide compelling evidence for delineation of the two species, B. hinzii – from poultry, humans and rabbit – and Bordetella pseudohinzii sp. nov. type strain 8-296-03^T (=NRRL B-59942^T=NCTC 13808^T) that infect mice.

Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species

Background

The genus Bordetella consists of nine species that include important respiratory pathogens such as the ‘classical’ species B. bronchiseptica, B. pertussis and B. parapertussis and six more distantly related and less extensively studied species. Here we analyze sequence diversity and gene content of 128 genome sequences from all nine species with focus on the evolution of virulence-associated factors.

Results

Both genome-wide sequence-based and gene content-based phylogenetic trees divide the genus into three species clades. The phylogenies are congruent between species suggesting genus-wide co-evolution of sequence diversity and gene content, but less correlated within species, mainly because of strain-specific presence of many different prophages. We compared the genomes with focus on virulence-associated genes and identified multiple clade-specific, species-specific and strain-specific events of gene acquisition and gene loss, including genes encoding O-antigens, protein secretion systems and bacterial toxins. Gene loss was more frequent than gene gain throughout the evolution, and loss of hundreds of genes was associated with the origin of several species, including the recently evolved human-restricted B. pertussis and B. holmesii, B. parapertussis and the avian pathogen B. avium.

Conclusions

Acquisition and loss of multiple genes drive the evolution and speciation in the genus Bordetella, including large scale gene loss associated with the origin of several species. Recent loss and functional inactivation of genes, including those encoding pertussis vaccine components and bacterial toxins, in individual strains emphasize ongoing evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3112-5) contains supplementary material, which is available to authorized users.

Effects of copper deficiency and copper toxicity on organogenesis and some physiological and biochemical responses of Scots pine (Pinus sylvestris L.) seedlings grown in hydroculture

The morphological, physiological, and biochemical parameters of 6-week-old seedlings of Scots pine (Pinus sylvestris L.) were studied under deficiency (1.2 nM) and chronic exposure to copper (0.32, 1, 2.5, 5, and 10 μM CuSO4) in hydroculture. The deposit of copper in the seed allowed the seedlings to develop under copper deficiency without visible disruption of growth. The high sensitivity of Scots pine to the toxic effects of copper was shown, which manifested as a significant inhibition of growth and development. The loss of dominance of the main root and a strong inhibition of lateral root development pointed to a lack of adaptive reorganization of the root system architecture under copper excess. A preferential accumulation of copper in the root and a minor translocation in aerial organs confirmed that Scots pine belongs to a group of plants that exclude copper. Selective impairment in the absorption of manganese was discovered, under both deficiency and excess of copper in the nutrient solution, which was independent of the degree of development of the root system. Following 10 μM CuSO4 exposure, the absorption of manganese and iron from the nutrient solution was completely suppressed, and the development of seedlings was secured by the stock of these micronutrients in the seed. The absence of signs of oxidative stress in the seedling organs was shown under deficiency and excess of copper, as evidenced by the steady content of malondialdehyde and 4-hydroxyalkenals. Against this background, no changes in total superoxide dismutase activity in the organs of seedlings were revealed, and the increased content of low-molecular-weight antioxidants was observed in the roots under 1 μM and in the needles under 5 μM CuSO4 exposures.

Effects of zinc on Scots pine (Pinus sylvestris L.) seedlings grown in hydroculture

The 6-week-old seedlings of Scots pine (Pinus sylvestris L.) showed high sensitivity to chronic exposure to zinc in hydroculture, which manifested in a significant inhibition of growth. Changes in the architecture of the root system and the suppression of its growth were shown to be the most striking effects of the toxic effect of zinc. Based on the data relating to the accumulation of zinc predominantly in the root system (by up to 35 times at 300 μM ZnSO4) and to the reduction in its translocation into the aerial organs, we concluded that P. sylvestris is related to a group of plants that exclude zinc. The seedlings developed a manganese deficiency (revealed by a reduction in Mn content in the roots and needles of up to 3.5 times at 300 μM ZnSO4) but not an iron deficiency (revealed by an increase in iron content of up to 23.7% in the roots and up to 42.3% in the needles at average). The absence of signs of oxidative stress under the effect of the zinc was detected as evidenced by the reduction in the content of malondialdehyde and 4-hydroxyalkenals in the seedling organs. The leading role of low molecular weight antioxidants in the prevention of oxidative stress in the seedling organs was suggested. Under the influence of zinc, a significant increase in the Trolox Equivalent Antioxidant Capacity of ethanol extracts of the seedling organs was found, which was caused by an increase in the total content of (+)-catechin and proanthocyanidins.

Growth in Egg Yolk Enhances Salmonella Enteritidis Colonization and Virulence in a Mouse Model of Human Colitis

Salmonella Enteritidis (SE) is one of the most common causes of bacterial food-borne illnesses in the world. Despite the SE's ability to colonize and infect a wide-range of host, the most common source of infection continues to be the consumption of contaminated shell eggs and egg-based products. To date, the role of the source of SE infection has not been studied as it relates to SE pathogenesis and resulting disease. Using a streptomycin-treated mouse model of human colitis, this study examined the virulence of SE grown in egg yolk and Luria Bertani (LB) broth, and mouse feces collected from mice experimentally infected with SEE1 (SEE1 passed through mice). Primary observations revealed that the mice infected with SE grown in egg yolk displayed greater illness and disease markers than those infected with SE passed through mice or grown in LB broth. Furthermore, the SE grown in egg yolk achieved higher rates of colonization in the mouse intestines and extra-intestinal organs of infected mice than the SE from LB broth or mouse feces. Our results here indicate that the source of SE infection may contribute to the overall pathogenesis of SE in a second host. These results also suggest that reservoir-pathogen dynamics may be critical for SE's ability to establish colonization and priming for virulence potential.

A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

Background

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR.

Methods

The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR.

Results

Here we describe a novel Type II-C CRISPR and its associated genes—cas1, cas2, and cas9—in several isolates of a newly discovered Bordetella species. The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii.

Conclusions

Expression of the CRISPR-Cas system and processing of crRNAs with perfect homology to prophages present in closely related species, but absent in that containing this CRISPR-Cas system, suggest it provides protection against phage predation. The 3,117-bp cas9 endonuclease gene from this novel CRISPR-Cas system is 990 bp smaller than that of Streptococcus pyogenes, the 4,017-bp allele currently used for genome editing, and which may make it a useful tool in various CRISPR-Cas technologies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2028-9) contains supplementary material, which is available to authorized users.

Host Specificity of Ovine Bordetella parapertussis and the Role of Complement

The classical bordetellae are comprised of three subspecies that differ from broad to very limited host specificity. Although several lineages appear to have specialized to particular host species, most retain the ability to colonize and grow in mice, providing a powerful common experimental model to study their differences. One of the subspecies, Bordetella parapertussis, is composed of two distinct clades that have specialized to different hosts: one to humans (Bpp_hu), and the other to sheep (Bpp_ov). While Bpp_hu and the other classical bordetellae can efficiently colonize mice, Bpp_ov strains are severely defective in their ability to colonize the murine respiratory tract. Bpp_ov genomic analysis did not reveal the loss of adherence genes, but substantial mutations and deletions of multiple genes involved in the production of O-antigen, which is required to prevent complement deposition on B. bronchiseptica and Bpp_hu strains. Bpp_ov lacks O-antigen and, like O-antigen mutants of other bordetellae, is highly sensitive to murine complement-mediated killing in vitro. Based on these results, we hypothesized that Bpp_ov failed to colonize mice because of its sensitivity to murine complement. Consistent with this, the Bpp_ov defect in the colonization of wild type mice was not observed in mice lacking the central complement component C3. Furthermore, Bpp_ov strains were highly susceptible to killing by murine complement, but not by sheep complement. These data demonstrate that the failure of Bpp_ov to colonize mice is due to sensitivity to murine, but not sheep, complement, providing a mechanistic example of how specialization that accompanies expansion in one host can limit host range.

Novel, host-restricted genotypes of Bordetella bronchiseptica associated with phocine respiratory tract isolates

During a succession of phocine morbillivirus outbreaks spanning the past 25 years, Bordetella bronchiseptica was identified as a frequent secondary invader and cause of death. The goal of this study was to evaluate genetic diversity and the molecular basis for host specificity among seal isolates from these outbreaks. MLST and PvuII ribotyping of 54 isolates from Scottish, English or Danish coasts of the Atlantic or North Sea revealed a single, host-restricted genotype. A single, novel genotype, unique from that of the Atlantic and North Sea isolates, was found in isolates from an outbreak in the Caspian Sea. Phylogenetic analysis based either on MLST sequence, ribotype patterns or genome-wide SNPs consistently placed both seal-specific genotypes within the same major clade but indicates a distinct evolutionary history for each. An additional isolate from the intestinal tract of a seal on the south-west coast of England has a genotype otherwise found in rabbit, guinea pig and pig isolates. To investigate the molecular basis for host specificity, DNA and predicted protein sequences of virulence genes that mediate host interactions were used in comparisons between a North Sea isolate, a Caspian Sea isolate and each of their closest relatives as inferred from genome-wide SNP analysis. Despite their phylogenetic divergence, fewer nucleotide and amino acid substitutions were found in comparisons of the two seal isolates than in comparisons with closely related strains. These data indicate isolates of B. bronchiseptica associated with respiratory disease in seals comprise unique, host-adapted and highly clonal populations.

Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan

Commercial poultry is an important agricultural industry worldwide. Although dense living conditions and large flocks increase meat and egg production, they also increase the risk of disease outbreaks and zoonoses. Current pathogen identification methods mostly rely on culture-dependent techniques and, therefore, are limited to a very small number of bacteria present in the environment. Next Generation Sequencing allows for culture-independent characterization of lower respiratory microbiome of birds including the identification of novel commensals and potentially emerging pathogens. In this study, we collected tracheo-bronchoalveolar lavage of 14 birds raised at 3 different farms in the Punjab province of Pakistan. To characterize the lower respiratory microbiome of these birds, we sequenced hyper-variable regions of the 16S ribosomal subunit gene. Although dominated by bacteria belonging to a small number of taxonomic classifications, the lower respiratory microbiome from each farm was far more diverse and novel than previously known. The differences in microbiome among farms suggest that inter-farm differences affect the microbiome of birds more than breed, geographic location, or management system. The presence of potential and known pathogens in genetically similar specialty breeds of chickens kept at unnaturally high densities and under variable conditions presents an extraordinary opportunity for the selection of highly pathogenic bacteria. In some instances, opportunistic respiratory pathogens were observed in apparently healthy birds. Understanding and monitoring the respiratory microbiome of such populations may allow the early detection of future disease threats.

Ballistic thermoelectric transport in a Luttinger liquid

The Seebeck and Peltier coefficients of a homogeneous Luttinger liquid are calculated in the ballistic regime. Nonlinearity of the electron spectrum is taken into account. It is shown that, in the framework of the defined approximations, the thermoelectric power of a Luttinger liquid is equal to zero, in agreement with the exponentially small thermopower of a one-dimensional degenerate Fermi gas. The Peltier coefficient is controlled by a nonequilibrium state of the system. It is finite and renormalized by the interaction in the case of a convective flow of a Luttinger liquid. The zero modes of bosonic excitations and the dispersion-induced contribution to the electric current operator are taken into account in calculations.

70-S ribosomes of Escherichia coli have an additional site for deacylated tRNA binding

Escherichia coli 70-S ribosomes contain a third site for tRNA binding, additional to the A and P sites. This conclusion is based on several findings. Direct measurements showed that in the presence of poly(U), when both A and P sites are occupied by Ac[14C]Phe-tRNAPhe, ribosomes are capable of binding additionally deacylated non-cognate [3H]tRNA. If ribosomes in the preparation are active enough, the total binding of labeled ligands amounted to 2.5 mol/mol ribosomes. In the absence of poly(U), when the A site can not bind, the P site and the 'additional' site can be filled simultaneously with Ac[14C]Phe-tRNAPhe and deacylated [3H]tRNA, or with [3H]tRNA alone; the total binding exceeds in this case 1.5 mol/mol ribosomes. The binding at the 'additional' site is not sensitive to the template. [3H]tRNA bound there is able to exchange rapidly for unlabeled tRNA in solution. Deacylated tRNA is preferred to the aminoacylated one. The binding of AcPhe-tRNAPhe was not observed there at all. The 3'-end adenosine is essential for the affinity. The function of the 'additional' site is not known, but its existence has to be considered when tRNA . ribosome complexes are studied.

On the mechanism of interaction of N-acetylphenylalanyl-tRNAPhe with ribosomes of Escherichia coli: effect of antibiotics and Tp psi pCpGp

The tetranucleotide Tp psi pCpGp acts as a specific inhibitor of the rate of AcPhe-tRNAPhe binding in the ribosomal P site. This effect is observed both in the presence and in the absence of poly(U). In the absence of poly(U) antibiotics tetracycline and puromycin also decrease the rate of AcPhe-tRNAPhe binding. Some inhibition by tetracycline is observed with poly(U). All these inhibitors are known to be ligands of the ribosomal A site, and their influence on the P site binding can be most naturally explained by the suggestion that AcPhe-tRNAPhe enters the ribosome via the A site, forms there an intermediate complex, and spontaneous translocation into the P site follows. In the presence of poly(U) arguments in favour of this hypothesis are much weaker, but the same sequence of events is possible.

Quantitative study of the interaction of formylmethionyl-tRNAfMet with ribosomes of Escherichia coli

fMet-tRNAfMet binds reversibly to the donor site (P-site) of Escherichia coli ribosomes both in the absence of messenger and in the presence of ApUpGp and some other oligonucleotides or poly(U). Kinetics of interaction conforms the second-order law. The equilibrium constants and the rate constants of binding are estimated at 0 degrees C. Not only the cognate trinucleotide ApUpGp but also some other oligonucleotides and even poly(U) stimulate the binding. The presence of total deacylated tRNA considerably increases the selectivity of association.

Interaction of transfer RNA with 50S ribosomal subunits of Escherichia coli in absence of templates

The equilibrium constant of a complex of tRNA with the 50S ribosomal subunit was measured in the absence of a template. It was shown that the stability of the complex increases with an increase in the concentration of Mg2+, it decreases with an increase in the concentration of univalent ions, and does not depend on the pH of the medium in the range of 7.0-8.2. Removal of the 3'-terminal nucleoside of tRNA weakens the association approximately 40-fold; the subsequent successive splitting off of another three nucleotides has little effect on the association constant. In 90% 2H2O the stability of the complex increases approximately four-fold, which points to the large contribution of the hydrogen bonds to the free energy of the interaction. The tetranucleotide TphiCG competes slightly with tRNA for sites on the 50S subparticles; this means that the TphiC segment of tRNA does not play an important role in the formation of the complex under investigation.