Zubair Aslam

Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil

A Gram-reaction-negative, catalase- and oxidase-positive, aerobic, non-motile, light yellow and rod-shaped bacterium (designated Gsoil 809T) isolated from soil of ginseng field, was characterized by a polyphasic approach to clarify its taxonomic position. Strain Gsoil 809T was observed to grow optimally at 30 °C and at pH 7.0 on nutrient agar medium. Strain Gsoil 809T possessed β-glucosidase activity, which was responsible for its ability to transform protopanaxatriol-type ginsenoside Rg1 to ginsenoside Rh1. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Gsoil 809T belongs to the genus Arachidicoccus of the family Chitinophagaceae and was most closely related to Arachidicoccusrhizosphaerae Vu-144T (98.1 % 16S rRNA gene sequence similarity). The DNA G+C content was 39.4 mol%. The DNA-DNA hybridization value between strain Gsoil 809T and A.rhizosphaerae Vu-144T was 41.27±1.03 %. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3, which supported the affiliation of Gsoil 809T to the genus Arachidicoccus. Strain Gsoil 809T contained homospermidineas the major polyamine. Moreover, the physiological and biochemical test results and low DNA-DNA relatedness value allowed the phenotypic and genotypic differentiation of strain Gsoil 809T from recognized species of the genus Arachidicoccus. Therefore, strain Gsoil 809T represents a novel species of the genus Arachidicoccus, for which the name Arachidicoccus ginsenosidivorans sp. nov. is proposed. The type strain is Gsoil 809T (=KCTC 22820T=JCM 30984T).

Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost.

A Gram-stain-negative, strictly aerobic, non-motile, light yellow, short-rod bacterium (designated GJ30-7T) isolated from compost, was characterized using a polyphasic approach, in order to clarify its taxonomic position. Strain GJ30-7T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain Gsoil GJ30-7T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (the two main active components of ginseng) to ginsenoside F2. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that GJ30-7T belongs to the genus Sphingobacterium of the family Sphingobacteriaceae and was most closely related to Sphingobacterium yanglingense JCM 30166T (92.6 %), Sphingobacterium psychroaquaticum KACC 18188T (92.6 %), and Sphingobacterium thermophilum KCTC 23708T (92.0 %). The DNA G+C content was 43 mol% and MK-7 was the major isoprenoid quinone. The main polar lipids were phosphatidylethanolamine, one unidentified phospolipid and one unknown polar lipid. In contrast to standard and reference strains, unidentified sphingolipid was also present. The predominant fatty acids of strain GJ30-7T were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (summed feature 9), supporting the affiliation of strain GJ30-7T to the genus Sphingobacterium. However, strain GJ30-7T could be distinguished genotypically and phenotypically from species of the genus Sphingobacterium with validly published names. The novel isolate therefore represents a novel species, for which the name Sphingobacterium jejuense sp. nov. is proposed, with the type strain GJ30-7T (=KACC 18625T=JCM 30948T).

Phytoremediation of Arsenic-Contaminated Soils Using Arsenic Hyperaccumulating Ferns

Arsenic contamination of soils is a global environmental, agricultural, and health issue given to the toxic and carcinogenic nature of As. Several anthropogenic activities, such as mining and smelting, coal combustion, wood preservation, leather tanning operations, and use of As-based pesticides in agriculture, have led to elevated concentrations of As in soil. Therefore, remediation and restoration of As-contaminated soils is imperative for providing safe food and healthy soils. In contrast to conventional (physicochemical) remediation methods, phytoremediation of As-contaminated soils using As-hyperaccumulating fern species has emerged as an eco-friendly, cost-effective, and efficient technology. Since the discovery of As-hyperaccumulator, Pteris vittata L., several other As-hyperaccumulating fern species have been identified in Pteris and Pityrogramma genera which demonstrated the ability to remove As from soil. This review will briefly discuss about the As dynamics and availability in soil; elucidate the mechanisms involved in As tolerance and (hyper)accumulation by ferns/plants for improving the phytoremediation efficiency; evaluate the capacity of As-hyperaccumulating fern species (e.g., P. vittata, Pityrogramma calomelanos) for phytoremediation of As-contaminated soils under pot and field conditions; and discuss how phosphate amendments, microbes, and agronomic practices can increase phytoremediation efficiency of the ferns.

Zinc biofortification in rice: leveraging agriculture to moderate hidden hunger in developing countries

ABSTRACT A restricted dietary range and a deficit of essential minerals such as zinc (Zn) characterize the diets of under-nourished people. Zn deficiency is a global nutritional problem and intensity of the issue is even severe in developing countries. Cereal grains are key to fulfill a person’s daily energy requirements, but they have very low grain Zn concentrations, especially when grown in Zn-deficient soils. Zinc deficiency can be addressed in several ways viz., nutritional diversification, food enrichment and biofortification. Several limitations regarding nutritional diversification and food enrichment favored Zn biofortification as a perpetual solution of malnutrition. Among the potential biofortification options to rectify Zn deficiency, plant breeding approaches and agronomic biofortification offers major advantage. Current review appraised the possible role of Zn in plants, its uptake, translocation and partitioning efficiencies in cereal grains that is driven by various agronomic, breeding and biotechnological approaches. Moreover, review also discussed Zn application methods, Zn-phosphate hostility and indicators of Zn bioavailability which may improve Zn-use efficiency in rice. There is a genuine need to integrate Zn in rice production systems by using agronomic and conventional breeding tools. Likewise, agronomic biofortification is economically sustainable and practically adoptable solution to overcome the Zn deficiency issue in rice.

Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana

The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plants sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.

Cadmium toxicity and soil biological index under potato (Solanum tuberosum L.) cultivation

Increasing cadmium (Cd) pollution in soil is of great concern. A pot experiment was conducted with the aim of assessing the effect of Cd on soil biological indices under potato cultivation. Cadmium was added to 10 kg soil in each pot (6 seeds pot–1) as Cd(NO3)2 at 0, 15, 30, 45 and 60 mg kg–1 with three replications. All soil and plant parameters decreased with all Cd treatments; however, high levels of Cd had a significant (P < 0.05) suppressive effect. The highest Cd level significantly (P < 0.05) decreased microbial biomass carbon (2.16-fold), nitrogen (11.37-fold) and phosphorus (10.3-fold), as well as enzyme activities of dehydrogenase (4.36-fold), phosphatase (9.23-fold), and urease (9.61-fold). The highest Cd level also decreased pH (1.46-fold), potato shoot (3.55-fold) and root (7.43-fold) length, root (10.9-fold) and shoot (6.04-fold) fresh weight, root (7.51-fold) and shoot (13.7-fold) dry weight, chlorophyll content (27.0-fold), carotenoid content (4.08-fold), and plant macronutrient and micronutrient uptake in potato root and shoots. Conversely, the highest level of Cd significantly (P < 0.05) increased the biomass C : N (5.27-fold) and C : P (4.77-fold) ratios, soil extractable Cd (5.38-fold), and Cd uptake in potato root (5.05-fold) and shoot (4.82-fold) at the end of the experiment (day 60). Cadmium contamination substantially affected soil biological indices and growth of potato, and the Cd threshold was strongly associated with the extent of Cd concentration and duration to accumulate. Soil microbial biomass, enzymatic activities, pH and potato physiological parameters could be used as a sensitive indicators to reflect environmental stresses in soil ecosystems.

Erratum to: Nitrospirillum irinus sp. nov., a diazotrophic bacterium isolated from the rhizosphere soil of Iris and emended description of the genus Nitrospirillum

A polyphasic approach was used to characterize a novel nitrogen-fixing bacterial strain, designated YC6995T, isolated from the rhizosphere soil of Iris ensata var. spontanea (Makino) Nakai inhabiting a wetland located at an altitude of 960 m on Jiri Mountain, Korea. Strain YC6995T cells were Gram-negative, and rod-shaped, with motility provided by a single polar flagellum. Optimal growth conditions were 30 °C and pH 7.0. The major fatty acids of strain YC6995T were C18:1ω7c, C18:1 2-OH and C16:0 3-OH. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids were phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified glycolipids. The genomic DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed strain YC6995T to form a phyletic lineage with Nitrospirillum amazonense DSM 2787T with a high sequence similarity (97.2 %), but it displayed low sequence similarity with other remotely related genera, including Azospirillum (<93 %), Rhodocista (93.1–93.4 %), and Skermanella (91.2–93.3 %) in the family Alphaproteobacteria. Based on the phenotypic, chemotaxonomic, and phylogenetic evidences, strain YC6995T represents a novel species within the genus Nitrospirillum, for which the name Nitrospirillum irinus sp. nov. is proposed. The type strain is YC6995T (= KACC 13777T = DSM 22198T). An emended description of the genus Nitrospirillum is also proposed.

Plant growth promoting rhizobacteria reduce aphid population and enhance the productivity of bread wheat

Plant growth promoting rhizobacteria increase plant growth and give protection against insect pests and pathogens. Due to the negative impact of chemical pesticides on environment, alternatives to these chemicals are needed. In this scenario, the biological methods of pest control offer an eco-friendly and an attractive option. In this study, the effect of two plant growth promoting rhizobacterial strains (Bacillus sp. strain 6 and Pseudomonas sp. strain 6K) on aphid population and wheat productivity was evaluated in an aphid susceptible (Pasban-90) and resistant (Inqlab-91) wheat cultivar. The seeds were inoculated with each PGPR strain, separately or the combination of both. The lowest aphid population (2.1 tiller−1), and highest plant height (85.8 cm), number of spikelets per spike (18), grains per spike (44), productive tillers (320 m−2), straw yield (8.6 Mg ha−1), and grain yield (4.8 Mg ha−1) were achieved when seeds were inoculated with Bacillus sp. strain 6 + Pseudomonas sp. strain 6K. The grain yield of both varieties was enhanced by 35.5–38.9% with seed inoculation with both bacterial strains. Thus, the combine use of both PGPR strains viz. Bacillus sp. strain 6 + Pseudomonas sp. strain 6K offers an attractive option to reduce aphid population tied with better wheat productivity.

Biological control of broad-leaved dock infestation in wheat using plant antagonistic bacteria under field conditions

Conventional weed management systems have produced many harmful effects on weed ecology, human health and environment. Biological control of invasive weeds may be helpful to minimize these harmful effects and economic losses incurred to crops by weeds. In our earlier studies, plant antagonistic bacteria were obtained after screening a large number of rhizobacteria for production of phytotoxic substances and effects on wheat and its associated weeds under laboratory conditions. In this study, five efficient strains inhibitory to broad-leaved dock and non-inhibitory to wheat were selected and applied to broad-leaved dock co-seeded with wheat both in pot trial and chronically infested field trial. Effects of plant antagonistic bacteria on the weed and infested wheat were studied at tillering, booting and harvesting stage of wheat. The applied strains significantly inhibited the germination and growth of the weed to variable extent. Similarly, variable recovery in losses of grain and straw yield of infested wheat from 11.6 to 68 and 13 to 72.6% was obtained in pot trial while from 17.3 to 62.9 and 22.4 to 71.3% was obtained in field trial, respectively. Effects of plant antagonistic bacteria were also evident from the improvement in physiology and nutrient contents of infested wheat. This study suggests the use of these plant antagonistic bacteria to biologically control infestation of broad-leaved dock in wheat under field conditions.