Applied microbiology

Utilization of palm kernel cake for production of β-glucosidase by Aspergillus niger FTCC 5003 in solid substrate fermentation using an aerated column bioreactor

by Peyman Abdeshahian

Abdeshahian, P., Samat, N & Wan Yusoff, W.M. 2010.Biotechnology. 9:17-24.

Production of biofuel using biomass as a sustainable biological resource

by Peyman Abdeshahian

Abdeshahian, P., Ganjali Dashti, M., Kalil, M.S & Wan
Yusoff, W.M. 2010.Biotechnology. 9: 274-282.

Xylanase production by Aspergillus niger FTCC 5003 using palm kernel cake in fermentative bioprocess

by Peyman Abdeshahian

Abdeshahian, P., Samat, N & Wan Yusoff, W.M. 2009.Pakistan Journal of Biological Sciences. 12: 1049-1055.

Production of β-xylosidase by Aspergillus niger FTCC 5003 using palm kernel cake in a packed-bed bioreactor

by Peyman Abdeshahian

Abdeshahian, P., Samat, N & Wan Yusoff, W.M. 2010.Journal of Applied
Sciences. 10: 419-424.

Solid substrate fermentation for cellulase production using palm kernel cake as a renewable lignocellulosic source in packed-bed bioreactor

by Peyman Abdeshahian

Abdeshahian, P., Samat, N., Abdul Hamid, A & Wan Yusoff, W.M.
2011.Biotechnology. Bioprocess. Engineering . 16: 238-
244.

Solid substrate fermentation for cellulase production using palm kernel cake as a renewable lignocellulosic source in packed-bed bioreactor

by Peyman Abdeshahian

Abdeshahian, P., Samat, N., Abdul Hamid, A & Wan Yusoff, W.M.
2011.Biotechnology. Bioprocess. Engineering . 16: 238-
244.

Utilization of palm kernel cake for production of β-mannanase by Aspergillus niger FTCC 5003 in solid substrate fermentation using an aerated column bioreactor

by Peyman Abdeshahian

Abdeshahian, P., Samat, N., Abdul Hamid, A & Wan Yusoff, W.M.
2010.Journal of Industrial Microbiology &
Biotechnology 37: 103-109.

Antimicrobial properties of garlic oil against human enteric bacteria: evaluation of methodologies and comparisons with garlic oil sulfides and garlic powder

by Khattak Khushi

Modelling inactivation by aqueous chlorine dioxide of Dothiorella gregaria Sacc. and Fusarium tricinctum (Corda) Sacc. spores inoculated on fresh chestnut kernel

by Zhao Chen

Aims: To model survival curves of Dothiorella gregaria Sacc. and Fusarium tricinctum (Corda) Sacc. spores inoculated... more Aims: To model survival curves of Dothiorella gregaria Sacc. and Fusarium tricinctum (Corda) Sacc. spores inoculated on fresh chestnut kernel exposed to aqueous chlorine dioxide (ClO2).
Methods and Results: Spores of two dominant spoilage fungi, D. gregaria andF. tricinctum, were inoculated onto chestnut kernel and treated with ClO2. The inactivation efficacy of ClO2 treatment increased with ClO2 concentration and treatment time. The Weibull model was the best model to describe the ClO2 survival curves of D. gregaria, while the modified Gompertz model was most appropriate for fitting the survival curves of F. tricinctum. Within the range of ClO2 concentration from 3 to 7 mg l-1, the n values in the Weibull model were similar. The b value in the Weibull model and decimal logarithms of the M, B and C values in the modified Gompertz model had linear relationships with ClO2 concentration. After simplification, these two models still provided acceptable predictions.
Conclusion: Applying models for describing survival curves of fungal spores on chestnut kernel by aqueous ClO2 was feasible.
Significance and Impact of the Study: This work would promote the application of ClO2 sanitizing technique and mathematical models when preventingthe occurrence of chestnut kernel decay.

Identification of a red-pigmented bacterium producing a potent anti-tumor N-alkylated prodigiosin as Serratia marcescens

by Amit Deorukhkar

Effect of Multiwalled carbon nanotubes on viability and superoxide dismutase expression in human wound pathogens

by Sanjai Saxena

Recently, a wide variety of bionanocomposites and biocomposites are being developed to be used as extracellular matrix... more Recently, a wide variety of bionanocomposites and biocomposites are being developed to be used as extracellular matrix for chronic wound healing. Majority of the chronic wound situations arise due to infections caused by drug-resistant microbes like Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. In particular S. aureus has become refractory to the current armamentarium of antimicrobial drugs. Therefore, it is imperative while designing nanobiocomposites for use as extracellular matrices to profile their antimicrobial activity. MWNT (multi-wall carbon nanotube) has been exploited previously in designing biocompatible nanocomposite for medical applications. Keeping in view, we studied the antimicrobial effect of MWNT on human clinical burn/wound pathogens, which were Methicillin-resistant Staphylococci and one Vancomycin intermediate Staphylococcus  isolate. We also studied E. coli NCTC 10418 and Pseudomonas aeruginosa NCTC 10662, two surrogate gram negative microbes to understand their behavior in the presence of MWNT. Apart from reduction in viable counts of the test panel, organism's extracellular expression of the enzyme Superoxide dismutase (SOD) was also taken into account as this is the probable mechanism adopted by bacteria in general to survive and sustain under nutritional and other stress situation including pathogenesis. The present study indicated that all Staphylococcal isolates were susceptible to MWNT which reduced the bacterial count between 3–9 logs barring Sau G19 which only exhibited 1 log reduction. Sau G17, Sau G18, and Sau G19 expressed a higher SOD activity, Sau G9 exhibited a lower SOD expression and in Sau G16, the SOD expression was nearly the same as compared to control. Thus, from this study, it could be inferred that MWNT, apart from being antimicrobial, induces oxidative stress on S. aureus.

Effect of vernalization on grain fill duration and grain weight in spring wheat

by IFTIKHAR AHMED

Muhammad Iqbal, Muhammad Fayyaz, Armghan Shahzad, Iftikhar Ahmed, Ghulam Muhammad Ali, Muhammad Shahid Masood and Dean Spaner. Pak. J. Bot., 43(1): 689-694, 2011.

Vernalization response genes are known to contribute indirectly to grain yield by influencing flowering time, number... more Vernalization response genes are known to contribute indirectly to grain yield by influencing flowering time, number of tillers and spikelets in sensitive wheat genotypes. There has been no report of the effect of vernalization on grain fill duration and grain weight in wheat. The objective of this study was to investigate the effect of vernalization on grain fill duration and grain weight in a set of 5 high latitude spring wheat, differing in vernalization response, and their 10 F1 hybrids obtained from a one-way diallel cross. The 15 genotypes were grown with and without 42d-vernalization treatment. Vernalization altered grain fill duration and grain weight in both sensitive and in-sensitive genotypes and no clear pattern was observed in terms of the vernalization responsiveness of the genotypes. No correlation was found between grain fill duration and grain weight in vernalized and non-vernalized treatment, indicating that the increase in grain fill duration of some of the genotypes with vernalization did not have an effect on grain weight. In order to harvest the full yield potential, vernalization sensitive genotypes may be grown in those eco-regions of high northern latitudes where growing season is relatively long and where temperatures are usually above the vernalization range.

Antibiotic resistance plasmids in wastewater treatment plants and their possible dissemination into the environment

by Teddie Rahube

Teddie O. Rahube and Christopher K. Yost, published in African Journal of Biotechnology, December 2010

Allelic variation at the Vrn-A1, Vrn-B1, Vrn-D1, Vrn-B3 and Ppd-D1a loci of Pakistani spring wheat cultivars

by IFTIKHAR AHMED

Muhammad Iqbal, Armghan Shahzad and Iftikhar Ahmed, published in Electronic Journal of Biotechnology, Vol. 14, No. 1 (2011)

Flowering time in bread wheat (Triticum aestivum L.) is controlled by vernalization and photoperiod response, and... more Flowering time in bread wheat (Triticum aestivum L.) is controlled by vernalization and photoperiod response, and earliness per se genes. The genetic basis of flowering time has not been investigated in Pakistani bread wheat. This study was, therefore, conducted to determine the allelic composition at Vrn-A1, Vrn-B1, Vrn-D1, Vrn-B3 and Ppd-D1a loci of 59 Pakistani spring bread wheat cultivars. These cultivars, along with 4 isogenic lines for vernalization genes were characterized with previously reported DNA markers designed for detecting allelic variation at 4 Vrn and 1 Ppd loci. Spring habit Vrn-A1a allele was found in 36% cultivars either alone or with spring habit Vrn-B1 and Vrn-D1 alleles. Two wheat cultivars had the dominant Vrn-A1c allele, whereas none of the cultivars had Vrn-A1b. Spring habit Vrn-B1 was the most frequent allele (64%) present either alone or with Vrn-A1a, Vrn-A1c and Vrn-D1. Spring habit Vrn-D1 was found in 61% cultivars. Vrn-D1 was singly found in 25% cultivar, and along with Vrn-B1 in 29% cultivars. Dominant Vrn-B3 was absent in all cultivars studied. All cultivars except Era had the photoperiod insensitive allele Ppd-D1a . We did not find any association between the flowering time and Vrn allelic composition of the studied cultivars. This indicated that the partial vernalization requirement of cultivars with Vrn-B1 and Vrn-D1 alleles is probably fulfilled during Pakistani growing season. Earliness per se and the photoperiod sensitive loci other than Ppd-D1 need to be investigated to further understand the genetic basis of flowering time in Pakistani wheat.

Caractérisation Microbiologique De L'Argile à Opalinus Du Mont Terri Et De L'Argilite Du Callovo-Oxfordien De Meuse/Haute-Marne

by Sebastien Poulain

PhD Thesis, 2006

"Microbial investigations in Opalinus clay from Mont Terri and in Callovo-Oxfordian argilite from... more "Microbial investigations in Opalinus clay from Mont Terri and in Callovo-Oxfordian argilite from Meuse/Haute-Marne"

The subject of this Ph.D. thesis deals with research achieved in the context of the Axis 2 of the law Bataille voted on December 30, 1991 about the possibility of building a deep geological repository for medium or high activity and long living nuclear waste. Nearby such a site, some microorganisms may influence the mobility of radionuclides coming from the waste canisters. This work consisted in looking for autochthonous microorganisms in the Opalinus clay formation from Mont Terri (Switzerland) and in the Callovo-Oxfordian argilite from Meuse/Haute-Marne (France). Microbial Investigations in these unknown unperturbed environments suggested very low microbial densities in the clayey sediments. However, new bacterial species could be isolated from those samples. In addition, a part of the allochtonous population, which has been introduced by air and human activity, could be identified in the Meuse/Haute-Marne underground research laboratory.

Soil Beneficial Bacteria and Their Role In Plant Growth Promotion: a Review

by IFTIKHAR AHMED

Rifat Hayat, Safdar Ali, Ummay Amara, Rabia Khalid and Iftikhar Ahmed; 2010. Ann Microbiol DOI 10.1007/s13213-010-0117-1

Soil bacteria are very important in biogeochemical cycles and have been used for crop production for decades.... more Soil bacteria are very important in biogeochemical cycles and have been used for crop production for decades. Plant-bacterial interactions in the rhizosphere are the determinants of plant health and soil fertility. Free-living soil bacteria beneficial to plant growth, usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. PGPR are also termed plant health promoting rhizobacteria (PHPR) or nodule promoting rhizobacteria (NPR). These are associated with the rhizosphere, which is an important soil ecological environment for plant–microbe interactions. Symbiotic nitrogen-fixing bacteria include the cyanobacteria of the genera Rhizobium, Bradyrhizobium, Azorhizobium, Allorhizobium, Sinorhizobium and Mesorhizobium. Free-living nitrogen-fixing bacteria or associative nitrogen fixers, for example bacteria belonging to the species Azospirillum, Enterobacter, Klebsiella and Pseudomonas, have been shown to attach to the root and efficiently colonize root surfaces. PGPR have the potential to contribute to sustainable plant growth promotion. Generally, PGPR function in three different ways: synthesizing particular compounds for the plants, facilitating the uptake of certain nutrients from the soil, and lessening or preventing the plants from diseases. Plant growth promotion and development can be facilitated both directly and indirectly. Indirect plant growth promotion includes the prevention of the deleterious effects of phytopathogenic organisms. This can be achieved by the production of siderophores, i.e. small metal-binding molecules. Biological control of soil-borne plant pathogens and the synthesis of antibiotics have also been reported in several bacterial species. Another mechanism by which PGPR can inhibit phytopathogens is the production of hydrogen cyanide (HCN) and/or fungal cell wall degrading enzymes, e.g., chitinase and ß-1,3-glucanase. Direct plant growth promotion includes symbiotic and non-symbiotic PGPR which function through production of plant hormones such as auxins, cytokinins, gibberellins, ethylene and abscisic acid. Production of indole-3-ethanol or indole-3-acetic acid (IAA), the compounds belonging to auxins, have been reported for several bacterial genera. Some PGPR function as a sink for 1-aminocyclopropane-1-carboxylate (ACC), the immediate precursor of ethylene in higher plants, by hydrolyzing it into α-ketobutyrate and ammonia, and in this way promote root growth by lowering indigenous ethylene levels in the micro-rhizo environment. PGPR also help in solubilization of mineral phosphates and other nutrients, enhance resistance to stress, stabilize soil aggregates, and improve soil structure and organic matter content. PGPR retain more soil organic N, and other nutrients in the plant–soil system, thus reducing the need for fertilizer N and P and enhancing release of the nutrients.

Rhodococcus baikonurensis BTM4c, a boron-tolerant actinobacterial strain isolated from soil.

by IFTIKHAR AHMED

Yoon, J., H. Miwa, I. Ahmed, A. Yokota and T. Fujiwara. 2010. Biosci. Biotechnol.Biochem., 74 (1): 178-181.

Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.

by IFTIKHAR AHMED

Miwa, H., I. Ahmed, J. Yoon, A. Yokota and T. Fujiwara. 2008. Intl. J. Syst. Evol. Microbiol. 58(1): 286–289.

A non-spore-forming, Gram-negative, motile, rod-shaped, boron-accumulating bacterium isolated from soil was... more A non-spore-forming, Gram-negative, motile, rod-shaped, boron-accumulating bacterium isolated from soil was characterized by polyphasic taxonomy. The strain, designated BAM-48T, was positive for catalase and oxidase activities and grew at 4–37 6C, 0–1% NaCl and pH 5–9. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate BAM-48T was closely related to Variovorax paradoxus IAM 12373T (99.3% sequence similarity), Variovorax soli GH9-3T (98.3 %) and Variovorax dokdonensis DS-43T (97.0 %). DNA–DNA hybridization values between strain BAM-48T and V. paradoxus NBRC 15149T, V. soli KACC 11579T and V. dokdonensis KCTC 12544T were only 49.1, 25.4 and 24.6 %, respectively. The major respiratory quinone was ubiquinone 8 (Q-8). The DNA G+C content was 71.2 mol%. Strain BAM-48T contained C16 : 0 (36.1 %), C16 : 1v7c (21.4 %) and C17 : 0 cyclo (19.0 %) as the major fatty acids. Based on phenotypic, chemotaxonomic and phylogenetic data, strain BAM-48T should be classified as a member of a novel species in the genus Variovorax, for which the name Variovorax boronicumulans sp. nov. is proposed. The type strain is BAM-48T (NBRC 103145T 5KCTC 22010T).

Chimaereicella boritolerans sp. nov., a novel boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae, isolated from soil.

by IFTIKHAR AHMED

Ahmed, I., A. Yokota and T. Fujiwara. 2007.  Intl. J. Syst. Evol. Microbiol. 57 (5): 986–992.

A non-motile, Gram-negative, boron-tolerant and alkaliphilic bacterium was isolated from soil of the Hisarcik area in... more A non-motile, Gram-negative, boron-tolerant and alkaliphilic bacterium was isolated from soil of the Hisarcik area in the Kutahya Province of Turkey that was naturally high in boron minerals. The novel isolate, designated T-22T, formed rod-shaped cells, was catalase- and oxidase-positive and tolerated up to 300 mM boron. The strain also survived on agar medium containing up to 3% (w/v) NaCl. The pH range for growth of this strain was 6.5–10.0 (optimum pH 8.0–9.0) and the temperature range was 16–37C (optimum 28–30C). Phylogenetic analysis based on 16S rRNA gene sequences revealed a clear affiliation with the genus Chimaereicella, with 97.4% sequence similarity to Chimaereicella alkaliphila AC-74T, which was the highest similarity among cultivated bacteria. The DNA–DNA relatedness with C. alkaliphila AC-74T was 28.3 %. The major respiratory quinone system was MK-7 and the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 1v9c, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or iso-C16 : 1v7c). The DNA G+C content was 42.5 mol%. Based on the phylogenetic analysis and physiological, chemotaxonomic and genetic data, we concluded that strain T-22T should be classified in the genus Chimaereicella, and we propose the name Chimaereicella boritolerans sp. nov. for this novel species. The type strain is strain T-22T (=DSM 17298T=NBRC 101277T=ATCC BAA-1189T).

Lysinibacillus parviboronicapiens sp. nov., a low-boron-containing bacterium isolated from soil.

by IFTIKHAR AHMED

Miwa, H., I. Ahmed, A. Yokota and T. Fujiwara. 2009. Intl. J. Syst. Evol. Microbiol. 59: 1427-1432.

A spore-forming, Gram-positive-staining, motile, rod-shaped and low-boron-containing bacterium was isolated from soil.... more A spore-forming, Gram-positive-staining, motile, rod-shaped and low-boron-containing bacterium was isolated from soil. The strain, designated BAM-582T, can tolerate 6% (w/v) NaCl and 50 mM boron, but optimal growth was observed without addition of boron or NaCl. The optimum temperature and pH for growth were 30 6C (range 10–37 6C) and pH 7 (range pH 6–8). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strain was closely related to Lysinibacillus fusiformis DSM 2898T (97.7% similarity) and Lysinibacillus sphaericus IAM 13420T (98.2 %). Levels of DNA–DNA relatedness were 33.9% with L. fusiformis DSM 2898T and 29.5% with L. sphaericus DSM 28T. The genomic DNA G+C content of the novel strain was 38.7 mol%. The major respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0 (37.4 %) and anteiso-C15 : 0 (19.0 %). Analysis of cell-wall amino acids revealed that the strain contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid, as is the case with other species of the genus Lysinibacillus. Based upon its distinctive peptidoglycan composition, phylogenetic and genotypic analyses and physiological characteristics, the strain BAM-582T is concluded to represent a novel species in the genus Lysinibacillus, for which the name Lysinibacillus parviboronicapiens sp. nov. is proposed (type strain BAM-582T 5NBRC 103144T 5KCTC 13154T).