Sibdas Ghosh

Three newly isolated plant growth-promoting bacilli facilitate the seedling growth of canola, Brassica campestris

Abstract Three strains of plant growth-promoting bacteria were isolated from southeastern Wisconsin soils, based upon the ability to utilize the compound 1-aminocyclopropane-1-carboxylic acid (ACC) as a sole nitrogen source. These novel bacteria have been identified as Bacillus circulans DUC1, Bacillus firmus DUC2, and Bacillus globisporus DUC3. Each strain displayed similar levels of ACC deaminase activity (EC 4.1.99.4) and stimulated root elongation in canola (Brassica campestris) seedlings under gnotobiotic conditions. Soil inoculations with respective bacterial strains increased the root and shoot lengths and fresh and dry weights of potted canola plants. Similarly, a soil inoculation with B. globisporus DUC3 promoted root and shoot growth of plants subjected to a diurnal temperature regime. This is the first report of plant growth-promoting bacilli with the ability to catabolize ACC.

Release of Photosynthetic Protein Catabolites by Blebbing from Thylakoids

Thylakoid proteins and their catabolites have been detected in lipid-protein particles isolated from the stroma of intact chloroplasts obtained from primary leaves of 2-week-old bean seedlings (Phaseolus vulgaris L. cv Kinghorn). The lipid-protein particles bear morphological resemblance to plastoglobuli seen in the chloroplasts of senescing leaves, but they are much smaller. They range from 10 to 320 nm in radius, are uniformly stained in thin sections visualized by transmission electron microscopy, and are discernible in the stroma of chloroplasts in corresponding thin-sectioned leaf tissue. The lipid-protein particles contain thylakoid lipids and are enriched in free fatty acids. Specifically, the free-to-esterified fatty acid ratio is about 1:1 in the particles compared to only 1:18 for corresponding thylakoid membranes. Western blot analyses indicate that these particles also contain thylakoid proteins and, in some cases, catabolites of these proteins including the CF1 [beta] and [gamma] subunits of ATPase, cytochrome f, and the 31- and 33-kD proteins of PSII. Lipid-protein particles with similar properties were generated in vitro from isolated, light-stressed thylakoids. Collectively, these data suggest that blebbing of lipid-protein particles may be a means of removing potentially destabilizing macromolecular catabolites from thylakoid membrane bilayers.

Isolation and characterization of a Lysinibacillus strain B1-CDA showing potential for bioremediation of arsenics from contaminated water

The main objective of this study was to identify and isolate arsenic resistant bacteria that can be used for removing arsenic from the contaminated environment. Here we report a soil borne bacterium, B1-CDA that can serve this purpose. B1-CDA was isolated from the soil of a cultivated land in Chuadanga district located in the southwest region of Bangladesh. The morphological, biochemical and 16S rRNA analysis suggested that the isolate belongs to Lysinibacillus sphaericus. The minimum inhibitory concentration (MIC) value of the isolate is 500 mM (As) as arsenate. TOF-SIMS and ICP-MS analysis confirmed intracellular accumulation and removal of arsenics. Arsenic accumulation in cells amounted to 5.0 mg g−1 of the cells dry biomass and thus reduced the arsenic concentration in the contaminated liquid medium by as much as 50%. These results indicate that B1-CDA has the potential for remediation of arsenic from the contaminated water. We believe the benefits of implementing this bacterium to efficiently reduce arsenic exposure will not only help to remove one aspect of human arsenic poisoning but will also benefit livestock and native animal species. Therefore, the outcome of this research will be highly significant for people in the affected area and also for human populations in other countries that have credible health concerns as a consequence of arsenic-contaminated water.

In silico and in vivo studies of an Arabidopsis thaliana gene, ACR2, putatively involved in arsenic accumulation in plants.

AbstractPreviously, our in silico analyses identified four candidate genes that might be involved in uptake and/or accumulation of arsenics in plants: arsenate reductase 2 (ACR2), phytochelatin synthase 1 (PCS1) and two multi-drug resistant proteins (MRP1 and MRP2) [Lund et al. (2010) J Biol Syst 18:223–224]. We also postulated that one of these four genes, ACR2, seems to play a central role in this process. To investigate further, we have constructed a 3D structure of the Arabidopsis thaliana ACR2 protein using the iterative implementation of the threading assembly refinement (I-TASSER) server. These analyses revealed that, for catalytic metabolism of arsenate, the arsenate binding-loop (AB-loop) and residues Phe-53, Phe-54, Cys-134, Cys-136, Cys-141, Cys-145, and Lys-135 are essential for reducing arsenate to arsenic intermediates (arsenylated enzyme-substrate intermediates) and arsenite in plants. Thus, functional predictions suggest that the ACR2 protein is involved in the conversion of arsenate to arsenite in plant cells. To validate the in silico results, we exposed a transfer-DNA (T-DNA)-tagged mutant of A. thaliana (mutation in the ACR2 gene) to various amounts of arsenic. Reverse transcriptase PCR revealed that the mutant exhibits significantly reduced expression of the ACR2 gene. Spectrophotometric analyses revealed that the amount of accumulated arsenic compounds in this mutant was approximately six times higher than that observed in control plants. The results obtained from in silico analyses are in complete agreement with those obtained in laboratory experiments. FigureStudies of structure and function of Arabidopsis thaliana ACR2 protein by in silico and in vivo analyses. The iterative implementation of the threading assembly refinement (I-TASSER) server was used for constructing a 3D structure of ACR2 protein. In silico results suggest that the ACR2 protein is involved in conversion of arsenate to arsenite in the plant cells. Validation of the in silico results was performed by in vivo experiments.

Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics

Previously, we reported an arsenic resistant bacterium Lysinibacillus sphaericus B1-CDA, isolated from an arsenic contaminated lands. Here, we have investigated its genetic composition and evolutionary history by using massively parallel sequencing and comparative analysis with other known Lysinibacillus genomes. Assembly of the sequencing reads revealed a genome of ~4.5 Mb in size encompassing ~80% of the chromosomal DNA. We found that the set of ordered contigs contains abundant regions of similarity with other Lysinibacillus genomes and clearly identifiable genome rearrangements. Furthermore, all genes of B1-CDA that were predicted be involved in its resistance to arsenic and/or other heavy metals were annotated. The presence of arsenic responsive genes was verified by PCR in vitro conditions. The findings of this study highlight the significance of this bacterium in removing arsenics and other toxic metals from the contaminated sources. The genetic mechanisms of the isolate could be used to cope with arsenic toxicity.

Characterization of Thylakoid-Derived Lipid-Protein Particles Bearing the Large Subunit of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Lipid-protein particles bearing the 55-kD ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) (EC 4.1.1.39) large subunit (RLSU) and no detectable corresponding Rubisco small subunit (RSSU) were isolated from the stroma of intact chloroplasts by flotation centrifugation. Stromal RLSU-bearing particles appear to originate from thylakoids because they can also be generated in vitro by illumination of isolated thylakoids. Their formation in vitro is largely heat denaturable and is facilitated by light or ATP. RLSU-containing lipid-protein particles range from 0.05 to 0.10 [mu]m in radius, contain the same fatty acids as thylakoids, but have a 10- to 15-fold higher free-to-esterified fatty acid ratio than thylakoids. RLSU-bearing lipid-protein particles with no detectable RSSU were also immunopurified from the populations of both stromal lipid-protein particles and those generated in vitro from illuminated thylakoids. Protease shaving indicated that the RLSU is embedded in the lipid-protein particles and that there is also a protease-protected RLSU in thylakoids. These observations collectively indicate that the RLSU associated with thylakoids is released into the stroma by light-facilitated blebbing of lipid-protein particles. The release of RLSU-containing particles may in turn be coordinated with the assembly of Rubisco holoenzyme because chaperonin 60 is also associated with lipid-protein particles isolated from stroma.

Phytoremediation of arsenic from the contaminated soil using transgenic tobacco plants expressing ACR2 gene of Arabidopsis thaliana

We have cloned, characterized and transformed the AtACR2 gene (arsenic reductase 2) of Arabidopsis thaliana into the genome of tobacco (Nicotiana tabacum, var Sumsun). Our results revealed that the transgenic tobacco plants are more tolerant to arsenic than the wild type ones. These plants can grow on culture medium containing 200μM arsenate, whereas the wild type can barely survive under this condition. Furthermore, when exposed to 100μM arsenate for 35days the amount of arsenic accumulated in the shoots of transgenic plants was significantly lower (28μg/g d wt.) than that found in the shoots of non-transgenic controls (40μg/g d wt.). However, the arsenic content in the roots of transgenic plants was significantly higher (2400μg/g d. wt.) than that (2100μg/g d. wt.) observed in roots of wild type plants. We have demonstrated that Arabidopsis thaliana AtACR2 gene is a potential candidate for genetic engineering of plants to develop new crop cultivars that can be grown on arsenic contaminated fields to reduce arsenic content of the soil and can become a source of food containing no arsenic or exhibiting substantially reduced amount of this metalloid.

Steaming Inactivates Phytophthora ramorum, Causal Agent of Sudden Oak Death and Ramorum Blight, from Infested Nursery Soils in California

Schweigkofler, W., Kosta, K., Huffman, V., Sharma, S., Suslow, K., and Ghosh, S. 2014. Steaming inactivates Phytophthora ramorum, causal agent of Sudden Oak Death and ramorum blight, from infested nursery soils in California. Plant Health Progress doi:10.1094/PHP-RS-13-0111. Nursery trade plays a major role in the long-distance spread of Phytophthora ramorum, the causal agent of Sudden Oak Death (SOD) and ramorum blight of ornamental plants. Under federal regulations, nurseries found positive for P. ramorum must destroy infected plants and treat infested soils. The use of steam is an effective method to thermally inactivate P. ramorum from nursery soils as demonstrated at the National Ornamental Research Site at Dominican University (NORSDUC) and one commercial nursery in the Central Valley of California. Heating up the top soil layer (0-30 cm) to 50°C for 120 minutes resulted in complete thermal inactivation of P. ramorum. Consequently, the commercial nursery was released from federal quarantine. Steaming can be a fast, reliable and sustainable option for treating nursery soils.

In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells

This paper reports a continuation of our previous research on the phytochelatin synthase1 (PCS1) gene involved in binding and sequestration of heavy metals or metalloids in plant cells [1]. Construction of a 3D structure of the Arabidopsis thaliana PCS1 protein and prediction of gene function by employing iterative implementation of the threading assembly refinement (I-TASSER) revealed that PC ligands (3GC-gamma-glutamylcysteine) and Gln50, Pro53, Ala54, Tyr55, Cys56, Ile102, Gly161, His162, Phe163, Asp204 and Arg211 residues are essential for formation of chelating complex with cadmium (Cd2+) or arsenite (AsIII). This finding suggests that the PCS1 protein might be involved in the production of the enzyme phytochelatin synthase, which might in turn bind, localize, store or sequester heavy metals in plant cells. For validation of the in silico results, we included a T-DNA tagged mutant of Arabidopsis thaliana, SAIL_650_C12, (mutation in AtPCS1 gene) in our investigation. Furthermore, using reverse transcriptase PCR we confirmed that the mutant does not express the AtPCS1 gene. Mutant plants of SAIL_650_C12 were exposed to various amounts of cadmium (Cd2+) and arsenite (AsIII) and the accumulation of these toxic metals in the plant cells was quantified spectrophotometrically. The levels of Cd2+ and AsIII accumulation in the mutant were approximately 2.8 and 1.6 times higher, respectively, than that observed in the wild-type controlled plants. We confirmed that the results obtained in in silico analyses complement those obtained in in vivo experiments.

Bioremediation of hexavalent chromium (VI) by a soil-borne bacterium, Enterobacter cloacae B2-DHA

Chromium and chromium containing compounds are discharged into the nature as waste from anthropogenic activities, such as industries, agriculture, forest farming, mining and metallurgy. Continued disposal of these compounds to the environment leads to development of various lethal diseases in both humans and animals. In this paper, we report a soil borne bacterium, B2-DHA that can be used as a vehicle to effectively remove chromium from the contaminated sources. B2-DHA is resistant to chromium with a MIC value of 1000 µg mL−1 potassium chromate. The bacterium has been identified as a Gram negative, Enterobacter cloacae based on biochemical characteristics and 16S rRNA gene analysis. TOF-SIMS and ICP-MS analyses confirmed intracellular accumulation of chromium and thus its removal from the contaminated liquid medium. Chromium accumulation in cells was 320 µg/g of cells dry biomass after 120-h exposure, and thus it reduced the chromium concentration in the liquid medium by as much as 81%. Environmental scanning electron micrograph revealed the effect of metals on cellular morphology of the isolates. Altogether, our results indicate that B2-DHA has the potential to reduce chromium significantly to safe levels from the contaminated environments and suggest the potential use of this bacterium in reducing human exposure to chromium, hence avoiding poisoning.