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)).

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.

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.

Enhanced early nodulation of medicago truncatula co-inoculated with sinorhizobium medicae and achromobacter xylosoxidans

Efforts to increase the productivity and sustainability of agro-ecosystems have resulted in increased research focused on generating improved microbiological inoculant technologies. Plant growth-promoting rhizobacteria (PGPR) are one area receiving increased attention due to their potential for use as biofertilizers, plant-growth promoters, and biocontrol agents for weed and disease control in farming systems (Siddiqui, 2006).

Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

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.

Potential for agricultural production on disturbed soils mined for apatite using legumes and beneficial microbe

Christmas Island has been mined for rock phosphate for over 100 years, and as mining will finish in the next few decades there is a need to develop alternative economies on the island, such as high value crop production. However, to conserve the unique flora and fauna on the island, only land previously mined will be considered for this purpose. As these soils have been severely perturbed by mining, strategies to improve soil quality parameters need to be undertaken before plant based industries can be considered. For instance, legumes and beneficial microbes have demonstrated a positive role in the remediation of degraded soils. Therefore, this study aimed to establish the scientific basis upon which agriculture can effectively be developed on s oils post phosphate mining. Six legume species (Glycine max (Soybean), Vigna radiata (Mungbean), V. unguiculata (Cowpea), Phaseolus vulgaris (Navybean), Cajanus cajan (Pigeon pea), and Lablab purpureus (Lablab)) were sown onto a two ha rehabilitated site t hat had previously been mined for rock phosphate. The soil had a pH of 7.0, and was high in P but low in Bo, Cu, K, Mg, N and S and had low organic C. The legumes were inoculated with their respective rhizobial inoculant or co-inoculated with the rhizobia and a plant growth promoting bacteria (PGPB) at three different fertilizer rates (nil, a low rate, and five times the low rate). With the exception of P. vulgaris, all the legume species survived. The application of fertilizer was essential for maximum biomass yields 18 weeks after sowing, however the lower fertilizer rate was sufficient to obtain maximum yields for some cultivars. The PGPB increased yields and nodulation of some of the legumes at different fertilizer levels. Although the legumes (except P. vulgaris) grew in the Christmas Island environment, selection of appropriate legume cultivars and inoculants plus optimization of the fertilizer regime is required for reliable agricultural productivity on the island.

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.

Coiled polymeric growth factor gradients for multi-luminal neural chemotaxis

In the injured adult nervous system, re-establishment of growth-promoting molecular gradients is known to entice and guide nerve repair. However, incorporation of three-dimensional chemotactic gradients in nerve repair scaffolds, particularly in those with multi-luminal architectures, remains extremely challenging. We developed a method that establishes highly tunable three-dimensional molecular gradients in collagen-filled multi-luminal nerve guides by anchoring growth-factor releasing coiled polymeric fibers onto the walls of collagen-filled hydrogel microchannels. Differential pitch in the coiling of neurotrophin-eluting fibers generated sustained three-dimensional chemotactic gradients that appropriately induced the differentiation of Pheochromocytoma (PC12) cells into neural-like cells along an increasing concentration of nerve growth factor (NGF). Computer modeling estimated the stability of the molecular gradient within the luminal collagen, which we confirmed by observing the significant effects of neurotrophin gradients on axonal growth from dorsal root ganglia (DRG). Neurons growing in microchannels exposed to a NGF gradient showed a 60% increase in axonal length compared to those treated with a linear growth factor concentration. In addition, a two-fold increment in the linearity of axonal growth within the microchannels was observed and confirmed by a significant reduction in the turning angle ratios of individual axons. These data demonstrate the ability of growth factor-loaded polymeric coiled fibers to establish three-dimensional chemotactic gradients to promote and direct nerve regeneration in the nervous system and provides a unique platform for molecularly guided tissue repair.

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.

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.