A soil-free plant growth system to facilitate analysis of plant pathogen interactions in roots

Analysis of the interaction of pathogens with plant roots is often complicated by the growth of plants in a soil substrate. A soil-free plant growth system (SPS) was developed that removes the need for a substrate while supporting the growth of seedlings in a nutrient rich, oxygenated environment. The model legume Lupinus angustifolius was used to compare the growth of seedlings within soil and the SPS. Seedlings grown under both conditions were similar in morphology, anatomy and health (measured by leaf chlorophyll abundance) and importantly there was little difference in root growth and development although straighter and fuller root systems were achieved in the SPS. The ease of access to the root system proved efficient for the analysis of root and pathogen interactions with no interference from soil or adhering particulate matter. Following inoculation of L. angustifolius roots with Phytophthora cinnamomi the host/pathogen interaction was easily observed and tissues sampled undamaged.

Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo

The taxonomic status of a bacterium, strain NCCP-246(T), isolated from rhizosphere of Vigna mungo, was determined using a polyphasic taxonomic approach. The strain NCCP-246(T) can grow at 16-37 °C (optimum 32 °C), at pH ranges of 6-8 (optimum growth occurs at pH 7) and in 0-4 % (w/v) NaCl. Phylogenetic analysis based upon on 16S rRNA gene sequence comparison revealed that strain NCCP-246(T) belonged to genus Sphingobacterium. Strain NCCP-246(T) showed highest similarity to the type strain of Sphingobacterium canadense CR11(T) (97.67 %) and less than 97 % with other species of the genus. The DNA-DNA relatedness value of strain NCCP-246(T) with S. canadense CR11(T) and Sphingobacterium thalpophilum JCM 21153(T) was 55 and 44.4 %, respectively. The chemotaxonomic data revealed the major menaquinone as MK-7 and dominant cellular fatty acids were summed feature 3 [C16:1 ω7c/C16:1 ω6c] (37.07 %), iso-C15:0 (28.03 %), C16:0 (11.85 %), C17:0 cyclo (8.84 %) and C14:0 (2.42 %). The G+C content of the strain was 39.2 mol%. On the basis of DNA-DNA hybridization, phylogenetic analyses, physiological and, biochemical data, strain NCCP-246(T) can be differentiated from the validly named members of genus Sphingobacterium and thus represents as a new species, for which the name, Sphingobacterium pakistanensis sp. nov. is proposed with the type strain NCCP-246(T) (= JCM18974 (T) = KCTC 23914(T)).

Bacterial modes of action for enhancing of plant growth

The greatest issue affecting the sustainability of broad acre cropping both environmentally and economically is the requirement of fertilizers. These are based on mined phosphorous or other mineral ores, ammonia produced through the Harbour-Bosch process and industrially manufactured potash. As global demand for fertilizers increases, the costs associated with the production for each of these major nutrients increases. Biofertilizers such as plant growth promoting bacteria (PGPB) are a possible biotechnology that could alleviate the need for addition of increasing amounts of fertilizers. These bacteria naturally occur in soils and aggressively colonize around plant roots and have been shown to have plant growth promoting effects. PGPB are known to influence plant growth by various direct and indirect mechanisms; while some can affect plant physiology directly by mimicking synthesis of plant hormones,others increase mineral availability and nitrogen content in soil. Here we review the previously characterized modes of action for enhancement of plant growth by PGPB such as nitrogen fixation, nutrient solubilization and production of auxins and enzymes, as well as discussing more recent proposed modes of action such as secondary metabolites.

Compensatory growth in an aquatic plant mediates exploitative competition between seasonally tied herbivores

The degree to which vertebrate herbivores exploitatively compete for the same food plant may depend on the level of compensatory plant growth. Such compensation is higher when there is reduced density-dependent competition in plants after herbivore damage. Whether there is relief from competition may largely be determined by the life-history stage of plants under herbivory. Such stage-specific compensation may apply to seasonal herbivory on the clonal aquatic plant sago pondweed (Potamogeton pectinatus L.). It winters in sediments of shallow lakes as tubers that are foraged upon by Bewick's Swans (Cygnus columbianus bewickii Yarrell), whereas aboveground biomass in summer is mostly consumed by ducks, coots, and Mute Swans. Here, tuber predation may be compensated due to diminished negative density dependence in the next growth season. However, we expected lower compensation to summer herbivory by waterfowl and fish as density of aboveground biomass in summer is closely related to photosynthetic carbon fixation. In a factorial exclosure study we simultaneously investigated (1) the effect of summer herbivory on aboveground biomass and autumn tuber biomass and (2) the effect of tuber predation in autumn on aboveground biomass and tuber biomass a year later. Summer herbivory strongly influenced belowground tuber biomass in autumn, limiting food availability to Bewick's Swans. In contrast, tuber predation in autumn by Bewick's Swans had a limited and variable effect on P. pectinatus biomass in the following growth season. Whereas relief from negative density dependence largely eliminates effects of belowground herbivory by swans, aboveground herbivory in summer limits both above- and belowground plant biomass. Hence, there was an asymmetry in exploitative competition, with herbivores in summer reducing food availability for belowground herbivores in autumn, but not the other way around.

Mesoporous silica nanoparticles enhance seedling growth and photosynthesis in wheat and lupin

The application of mesoporous silica nanoparticles (MSNs) as a smart delivery system to agricultural crops is gaining attention but the release of nanoparticles into the environment may pose a potential threat to biological systems. We investigated the effects of MSNs on the growth and development of wheat and lupin plants grown under controlled conditions. We report a dramatic increase in the growth of wheat and lupin plants exposed to MSNs. We also found that, in leaves, MSNs localised to chloroplasts and that photosynthetic activity was significantly increased. In addition, absorption and cellular distribution of MSNs by the two plant species following root uptake were observed using scanning electron microscopy equipped with energy dispersive spectroscopy (SEM-EDS). Following uptake of MSNs at 500 and 1000 mg L(-1), there was enhancement of seed germination, increased plant biomass, total protein and chlorophyll content. Treatment of both species with MSNs at the highest concentration (2000 mg L(-1)) did not result in oxidative stress or cell membrane damage. These findings show that MSNs can be used as novel delivery systems in plants and that over the range of concentrations tested, MSNs do not have any negative impacts on plant growth or development.

Effects of down-regulating ornithine decarboxylase upon putrescine-associated metabolism and growth in Nicotiana tabacum L.

Transgenic plants of Nicotiana tabacum L. homozygous for an RNAi construct designed to silence ornithine decarboxylase (ODC) had significantly lower concentrations of nicotine and nornicotine, but significantly higher concentrations of anatabine, compared with vector-only controls. Silencing of ODC also led to significantly reduced concentrations of polyamines (putrescine, spermidine and spermine), tyramine and phenolamides (caffeoylputrescine and dicaffeoylspermidine) with concomitant increases in concentrations of amino acids ornithine, arginine, aspartate, glutamate and glutamine. Root transcript levels of S-adenosyl methionine decarboxylase, S-adenosyl methionine synthase and spermidine synthase (polyamine synthesis enzymes) were reduced compared with vector controls, whilst transcript levels of arginine decarboxylase (putrescine synthesis), putrescine methyltransferase (nicotine production) and multi-drug and toxic compound extrusion (alkaloid transport) proteins were elevated. In contrast, expression of two other key proteins required for alkaloid synthesis, quinolinic acid phosphoribosyltransferase (nicotinic acid production) and a PIP-family oxidoreductase (nicotinic acid condensation reactions), were diminished in roots of odc-RNAi plants relative to vector-only controls. Transcriptional and biochemical differences associated with polyamine and alkaloid metabolism were exacerbated in odc-RNAi plants in response to different forms of shoot damage. In general, apex removal had a greater effect than leaf wounding alone, with a combination of these injury treatments producing synergistic responses in some cases. Reduced expression of ODC appeared to have negative effects upon plant growth and vigour with some leaves of odc-RNAi lines being brittle and bleached compared with vector-only controls. Together, results of this study demonstrate that ornithine decarboxylase has important roles in facilitating both primary and secondary metabolism in Nicotiana.

Bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of Leclercia sp. QAU-66

Glucose dehydrogenase (GDH; EC 1.1. 5.2) is the member of quinoproteins group that use the redox cofactor pyrroloquinoline quinoine, calcium ions and glucose as substrate for its activity. In present study, Leclercia sp. QAU-66, isolated from rhizosphere of Vigna mungo, was characterized for phosphate solubilization and the role of GDH in plant growth promotion of Phaseolus vulgaris. The strain QAU-66 had ability to solubilize phosphorus and significantly (p ≤ 0.05) promoted the shoot and root lengths of Phaseolus vulgaris. The structural determination of GDH protein was carried out using bioinformatics tools like Pfam, InterProScan, I-TASSER and COFACTOR. These tools predicted the structural based functional homology of pyrroloquinoline quinone domains in GDH. GDH of Leclercia sp. QAU-66 is one of the main factor that involved in plant growth promotion and provides a solid background for further research in plant growth promoting activities.

Quantitation of ascorbic acid in Arabidopsis thaliana reveals distinct differences between organs and growth phases

Optimal plant growth is the result of the interaction of a complex network of plant hormones and environmental signals. Ascorbic acid (AsA) is a crucial antioxidant in plants and is involved in the regulation of cell division, cell expansion, photosynthesis and hormone biosynthesis. Quantitative analysis of AsA in Arabidopsis thaliana organs was conducted using HPLC with d -isoascorbic acid (Iso-AsA) as an internal standard. Analysis revealed Àuctuations in the levels of AsA in different organs and growth phases when plants were grown under standard conditions. AsA concentrations increased in leaves in direct proportion to leaf size and age. Young siliques (seed set stage) and Àowering buds (open and unopened) showed the highest levels of AsA. A relationship was found between the level of AsA and indole acetic acid (IAA) in leaves, stems, Àowers, and siliques and the highest level of IAA and AsAwere found in the Àowers. In contrast, the lowest level of the plant hormone, salicylic acid, was found in the Àowers and the highest quantity measured in the leaves. Consequently, AsA has been found to be a multifunctional molecule that is involved as a key regulator of plant growth and development.

Molecular identification and characterization of phosphate solubilizing pseudomonas sp. isolated from rhizosphere of mash bean (Vigna mungo L.) for growth promotion in wheat

Bio-inoculants have potential role in plant growth promotion. The present study evaluated the potential of Pseudomonas strains as bio-inoculants in wheat on the basis of plant growth promotion and physiological characterization. The 16S rRNA gene sequencing and phylogenetic analysis revealed that four isolated strains belonged to genus Pseudomonas. These strains were positive for phosphorus solubilization and indole acetic acid production, whereas only two strains were positive candidate for their nitrogen fixing ability as determined by presence or absence of nifH gene through amplification from polymerase chain reaction. The pot experiment showed that the integrated use of Pseudomonas strains as co-inoculant and 50% applied mineral fertilizers enhanced the maximum wheat growth and development from 58 to 140% for different shoot and root growth parameters. The strain NCCP-45 and NCCP-237 were closely related to Pseudomonas beteli and Pseudomonas lini, respectively. These isolated strains can be used to increase crop productivity by using as a bio-fertilizer inoculum.

Surface morphologies and internal fine structures of bast fibers

Fiber surface morphologies and associated internal structures are closely related to its properties. Unlike other fibers including cotton, bast fibers possess transverse nodes and fissures in cross-sectional and longitudinal directions. Their morphologies and associated internal structures were anatomically examined under the scanning electron microscope. The results showed that the morphologies of the nodes and the fissures of bast fibers varied depending on the construction of the inner fibril cellular layers. The transverse nodes and fissures were formed by the folding and spiralling of the cellular layers during plant growth. The dimensions of nodes and fissures were determined by the dislocations of the cellular layers. There were also many longitudinal fissures in bast fibers. Some deep longitudinal fissures even opened the fiber lumen for a short way along the fiber. In addition, the lumen channel of the bast fibers could be disturbed or disrupted by the nodes and the spirals of the internal cellular layers. The existence of the transverse nodes and fissures in the bast fibers could degrade the fiber mechanical properties, whereas the longitudinal fissures may contribute to the very rapid moisture absorption and desorption.

Children and terraira

The authors have been involved with a group of primary school children since 1998, exploring their science learning in the first years of school. This article describes an activity run with two classes in grade 1, focussing on their ideas about plants. The activity involves constructing a terrarium and using it to challenge children's ideas about the conditions for plant growth.

Investigation of compounds causing water repellency in the rhizosphere of sandy soils from a wide range of locations.

Although soils are generally considered to wet readily, some are actually water repellent at the surface and in the rhizosphere. This phenomenon occurs at low to moderate moisture contents and has been reported from soils under a range of vegetation types and from many regions around the globe. Water repellency in soils can have serious environmental implications including reduced seed germination and plant growth as well as irrigation efficiency, accelerated soil erosion, and enhanced leaching of agrochemicals through preferential flow. it has been proposed that water repellency is caused by the accumulation of hydrophobic organic compounds released as root exudates, microbial byproducts or from decomposing organic matter, which are deposited on mineral or aggregate surfaces, or are present as interstitial matter, Few studies to date have attempted to isolate and characterize these compounds and their structure is therefore only poorly understood, These studies have generally focussed on only a single soil or a small range of samples, have not included non-repellent soils as a control and have not always been able to demonstrate that the substances isolated are indeed responsible for repellency formation.

This study reports on the first part (extraction procedures) of a research programme addressing these gaps in current knowledge by investigating a wide range of severely repellent and wettable ‘control’ samples from different countries, and by including assessments of extraction efficiency and ability of extracts to cause repellency. Analytical methods include DRIFT (Diffuse Reflectance Infrared Fourier Transform Spectroscopy) of soils and IR (Infrared) analysis of extracts.

Key findings are that (i) soil sample heating after extraction is valuable in assessing the effectiveness of the extraction procedure, (ii) Soxhlet extraction using isopropanol/ ammonia (70/30 v/v) was the most effective method in extracting hydrophobic compounds, while leaving the ability of extracted compounds to induce water repellency virtually unaffected, (iii) wettable control soils also contain hydrophobic substances capable of inducing water repellency, (iv) the amount of organic compounds extracted was poorly related to sample repellency, indicating that compounds responsible for repellency may only represent a small fraction of the extract, (v) differences in extraction efficiency between different samples indicate that the compounds responsible may differ generically and/or in terms of their bonding to minerals, and (vi) the combination of repellency assessments with DRIFT on soils and JR on extracts used with internal standards has considerable potential to allow quantification of CH bearing organic matter in the soil, the efficiency of extraction processes for its removal, and its significance in causing water repellency in soils.

Spatial memory in a food storing corvid I. Near tall landmarks are primarily used

This work suggests how food storing corvids use spatial memory to relocate caches, and how they can do this after some landmarks surrounding caches have become hidden due to leaf fall, snow fall or plant growth. Experiments involved training European jays (Garrulus glandarius) to find buried food, the location of which was specified by an array of 12 landmarks. Tests were then performed with the array rotated, or with certain landmarks removed from the array. The.main findings were: (1) birds primarily remembered the position of the goal using the near tall landmarks (15-30 cm from the goal and 20 cm high); (2) birds obtained a sense of direction both from the landmark array and something external to the array; (3) birds did not use smell or marks in the surface of the ground to find the goal. Memory of near tall landmarks is likely to be functional for these birds since (a) nearer landmarks provide a more accurate fix, and (b) taller landmarks are less likely to be completely obscured by snow fall, leaf fall or intervening vegetation. The work also demonstrates the use of G.I.S. software for the analysis and representation of animal search patterns.

What decision rules might pink-footed geese use to depart on migration? An individual-based model

Decisions taken during migration can have a large effect on the fitness of birds. Migration must be accurately timed with food availability to allow efficient fueling but is also constrained by the optimal arrival date at the breeding site. The decision of when to leave a site can be driven by energetics (sufficient body stores to fuel flight), time-related cues (internal clock under photoperiodic control), or external cues (temperature, food resources). An individual based model (IBM) that allows a mechanistic description of a range of departure decision rules was applied to the spring migration of pink-footed geese (Anser brachyrhynchus) from wintering grounds in Denmark to breeding grounds on Svalbard via 2 Norwegian staging sites. By comparing predicted with observed departure dates, we tested 7 decision rules. The most accurate predictions were obtained from a decision rule based on a combination of cues including the amount of body stores, date, and plant phenology. Decision rules changed over the course of migration with the external cue decreasing in importance and the time-related cue increasing in importance for sites closer to breeding grounds. These results are in accordance with descriptions of goose migration, following the “green-wave”: Geese track the onset of plant growth as it moves northward in spring, with an uncoupling toward the end of the migration if time is running out. We demonstrate the potential of IBMs to study the possible mechanisms underlying stopover ecology in migratory birds and to serve as tools to predict consequences of environmental change.

Animal–plant–microbe interactions : direct and indirect effects of swan foraging behaviour modulate methane cycling in temperate shallow wetlands

Wetlands are among the most important ecosystems on Earth both in terms of productivity and biodiversity, but also as a source of the greenhouse gas CH₄. Microbial processes catalyzing nutrient recycling and CH₄ production are controlled by sediment physico-chemistry, which is in turn affected by plant activity and the foraging behaviour of herbivores. We performed field and laboratory experiments to evaluate the direct effect of herbivores on soil microbial activity and their indirect effects as the consequence of reduced macrophyte density, using migratory Bewick’s swans (Cygnus columbianus bewickii Yarrell) feeding on fennel pondweed (Potamogeton pectinatus L.) tubers as a model system. A controlled foraging experiment using field enclosures indicated that swan bioturbation decreases CH₄ production, through a decrease in the activity of methanogenic Archaea and an increased rate of CH₄ oxidation in the bioturbated sediment. We also found a positive correlation between tuber density (a surrogate of plant density during the previous growth season) and CH₄ production activity. A laboratory experiment showed that sediment sterilization enhances pondweed growth, probably due to elimination of the negative effects of microbial activity on plant growth. In summary, the bioturbation caused by swan grazing modulates CH₄ cycling by means of both direct and indirect (i.e. plant-mediated) effects with potential consequences for CH₄ emission from wetland systems.