Shams Tabrez Khan

Members of the Family Comamonadaceae as Primary Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate)-Degrading Denitrifiers in Activated Sludge as Revealed by a Polyphasic Approach

ABSTRACT The distribution and phylogenetic affiliations of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)-degrading denitrifying bacteria in activated sludge were studied by a polyphasic approach including culture-independent biomarker and molecular analyses as well as cultivation methods. A total of 23 strains of PHBV-degrading denitrifiers were isolated from activated sludges from different sewage treatment plants. 16S ribosomal DNA (rDNA) sequence comparisons showed that 20 of the isolates were identified as members of the family Comamonadaceae, a major group of β-Proteobacteria. When the sludges from different plants were acclimated with PHBV under denitrifying conditions in laboratory scale reactors, the nitrate removal rate increased linearly during the first 4 weeks and reached 20 mg NO3−-N h−1 g of dry sludge−1 at the steady state. The bacterial-community change in the laboratory scale sludges during the acclimation was monitored by rRNA-targeted fluorescence in situ hybridization and quinone profiling. Both approaches showed that the population of β-Proteobacteria in the laboratory sludges increased sharply during acclimation regardless of their origins. 16S rDNA clone libraries were constructed from two different acclimated sludges, and a total of 37 clones from the libraries were phylogenetically analyzed. Most of the 16S rDNA clones were grouped with members of the family Comamonadaceae. The results of our polyphasic approach indicate that β-Proteobacteria, especially members of the family Comamonadaceae, are primary PHBV-degrading denitrifiers in activated sludge. Our data provide useful information for the development of a new nitrogen removal system with solid biopolymer as an electron donor.

Streptomyces associated with a marine sponge Haliclona sp.; biosynthetic genes for secondary metabolites and products.

Terrestrial actinobacteria have served as a primary source of bioactive compounds; however, a rapid decrease in the discovery of new compounds strongly necessitates new investigational approaches. One approach is the screening of actinobacteria from marine habitats, especially the members of the genus Streptomyces. Presence of this genus in a marine sponge, Haliclona sp., was investigated using culture-dependent and -independent techniques. 16S rRNA gene clone library analysis showed the presence of diverse Streptomyces in the sponge sample. In addition to the dominant genus Streptomyces, members of six different genera were isolated using four different media. Five phylogenetically new strains, each representing a novel species in the genus Streptomyces were also isolated. Polyphasic study suggesting the classification of two of these strains as novel species is presented. Searching the strains for the production of novel compounds and the presence of biosynthetic genes for secondary metabolites revealed seven novel compounds and biosynthetic genes with unique sequences. In these compounds, JBIR-43 exhibited cytotoxic activity against cancer cell lines. JBIR-34 and -35 were particularly interesting because of their unique chemical skeleton. To our knowledge, this is the first comprehensive study detailing the isolation of actinobacteria from a marine sponge and novel secondary metabolites from these strains.

Sponge-derived Streptomyces producing isoprenoids via the mevalonate pathway

In the course of our screening program for isoprenoids of marine actinobacterial origin, 523 actinobacterial strains were isolated from marine samples. Actinobacteria usually use the 2-C-methyl-d-erythritol 4-phosphate pathway for the production of primary metabolites, but some have been reported to use the mevalonate (MVA) pathway for the production of isoprenoids as secondary metabolites. 3-Hydroxy-3-methyl glutaryl coenzyme A reductase (HMGR) is a key enzyme and plays an important role in the MVA pathway. Therefore, we screened strains possessing the HMGR gene from the 523 strains mentioned above and also investigated isoprenoid compounds from cultures of strains possessing HMGR genes. As a result, Streptomyces sp. SpC080624SC-11 isolated from a marine sponge, Cinachyra sp., was shown to possess the HMGR gene and produce novel isoprenoids, JBIR-46 (1), -47 (2), and -48 (3). On the basis of extensive NMR and MS analyses, the structures of 1-3 were determined to be phenazine derivatives harboring dimethylallyl moieties. Furthermore, the isoprene units of 2 and 3 were confirmed to be synthesized via the MVA pathway in a feeding experiment using [1-(13)C]acetate.

JBIR-31, a new teleocidin analog, produced by salt-requiring Streptomyces sp. NBRC 105896 isolated from a marine sponge.

JBIR-31, a new teleocidin analog, produced by salt-requiring Streptomyces sp. NBRC 105896 isolated from a marine sponge

New sesquiterpenes, JBIR-27 and -28, isolated from a tunicate-derived fungus, Penicillium sp. SS080624SCf1

In the course of our screening program for novel metabolites from tunicate-derived fungi, novel sesquiterpenoids, named JBIR-27 (1) and -28 (2), together with known sporogen-AO1 and phomenone, were isolated from the culture broth of Penicillium sp. SS080624SCf1. The structures of 1 and 2 were determined to be eremophilane analogs on the basis of extensive NMR and MS analyses. Sporogen-AO1, phomenone and 2 showed cytotoxicity against human cervical carcinoma cell line HeLa at IC50 values of 8.3, 19 and 92 μM, respectively, whereas 1 was inactive at a concentration of 80 μM.

Paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in Tokyo Bay.

Two novel marine, Gram-negative, non-motile, catalase- and oxidase-positive, aerobic bacteria were isolated from coastal seawater in Tokyo Bay. Analysis of almost-complete 16S rRNA gene sequences showed that the two isolates are members of the genus Paracoccus, sharing highest 16S rRNA gene sequence similarity (96.5 %) with Paracoccus aminophilus NBRC 16710(T). The DNA-DNA reassociation values between P. aminophilus NBRC 16710(T) and these isolates were only 10-20 %, in contrast to the high DNA relatedness between the two isolates (89 %). At least 1 % (w/v) NaCl was required for growth. Cellular fatty acid profiles revealed C(18 : 1)omega7c as the major component and C(10 : 0) 3-OH as the major hydroxy fatty acid. Ubiquinone-10 was detected as the major respiratory quinone. The G+C content of the genomic DNA of both strains was 69 mol%. On the basis of DNA-DNA hybridization data and physiological and chemotaxonomic characteristics, it is proposed that these strains should be placed in a novel species, Paracoccus marinus sp. nov. The type strain is KKL-A5(T) (=NBRC 100637(T) =CIP 108500(T)); KKL-B9 (=NBRC 100640) is a reference strain.

Countering drug resistance, infectious diseases, and sepsis using metal and metal oxides nanoparticles: Current status.

One fourth of the global mortalities is still caused by microbial infections largely due to the development of resistance against conventional antibiotics among pathogens, the resurgence of old infectious diseases and the emergence of hundreds of new infectious diseases. The lack of funds and resources for the discovery of new antibiotics necessitates the search for economic and effective alternative antimicrobial agents. Metal and metal oxide nanoparticles including silver and zinc oxide exhibit remarkable antimicrobial activities against pathogens and hence are one of the most propitious alternative antimicrobial agents. These engineered nanomaterials are approved by regulatory agencies such as USFDA and Koreas FITI, for use as antimicrobial agents, supplementary antimicrobials, food packaging, skin care products, oral hygiene, and for fortifying devices prone to microbial infections. Nevertheless, detailed studies, on molecular and biochemical mechanisms underlying their antimicrobial activity are missing. To take the full advantage of this emerging technology selective antimicrobial activity of these nanoparticles against pathogens should be studied. Optimization of these nanomaterials through functionalization to increase their efficacy and biocompatibility is also required. Urgent in vivo studies on the toxicity of nanomaterials at realistic doses are also needed before their clinical translation.

ZnO and TiO2 nanoparticles as novel antimicrobial agents for oral hygiene: a review

Oral cavity is inhabited by more than 25,000 different bacterial phylotypes; some of them cause systemic infections in addition to dental and periodontal diseases. Emergence of multiple antibiotic resistance among these bacteria necessitates the development of alternative antimicrobial agents that are safe, stable, and relatively economic. This review focuses on the significance of metal oxide nanoparticles, especially zinc oxide and titanium dioxide nanoparticles as supplementary antimicrobials for controlling oral infections and biofilm formation. Indeed, the ZnO NPs and TiO2 NPs have exhibited significant antimicrobial activity against oral bacteria at concentrations which is not toxic in in vivo toxicity assays. These nanoparticles are being produced at an industrial scale for use in a variety of commercial products including food products. Thus, the application of ZnO and TiO2 NPs as nanoantibiotics for the development of mouthwashes, dental pastes, and other oral hygiene materials is envisaged. It is also suggested that these NPs could serve as healthier, innocuous, and effective alternative for controlling both the dental biofilms and oral planktonic bacteria with lesser side effects and antibiotic resistance.

Antibacterial properties of silver nanoparticles synthesized using Pulicaria glutinosa plant extract as a green bioreductant.

The antibacterial properties of nanoparticles (NPs) can be significantly enhanced by increasing the wettability or solubility of NPs in aqueous medium. In this study, we investigated the effects of the stabilizing agent on the solubility of silver NPs and its subsequent effect on their antimicrobial activities. Silver NPs were prepared using an aqueous solution of Pulicaria glutinosa plant extract as bioreductant. The solution also acts as a capping ligand. During this study, the antimicrobial activities of silver NPs, as well as the plant extract alone, were tested against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Micrococcus luteus. Silver NPs were prepared with various concentrations of the plant extract to study its effect on antimicrobial activity. Interestingly, various concentrations of P. glutinosa extract did not show any effect on the growth of tested bacteria; however, a significant effect on the antimicrobial property of plant extract capped silver NPs (Ag-NPs-PE) was observed. For instance, the half maximal inhibitory concentration values were found to decrease (from 4% to 21%) with the increasing concentrations of plant extract used for the synthesis of Ag-NPs-PE. These results clearly indicate that the addition of P. glutinosa extracts enhances the solubility of Ag-NPs-PE and, hence, increases their toxicity against the tested microorganisms.

Streptomyces tateyamensis sp. nov., Streptomyces marinus sp. nov. and Streptomyces haliclonae sp. nov., isolated from the marine sponge Haliclona sp.

Three Gram-positive, NaCl-requiring actinobacteria were isolated from a marine sponge, Haliclona sp., collected from the coast of Tateyama City, Japan. Comparison of 16S rRNA gene sequences indicated that these strains represent novel members of the genus Streptomyces, exhibiting low 16S rRNA gene sequence similarities of 98.3-97.4 % with recognized members of the genus. The cell hydrolysates contained the LL-isomer of diaminopimelic acid and the predominant quinones were MK-9 (H(6) and/or H(8)). The DNA G+C contents were in the range 72-75mol%. A polyphasic study of the strains and comparison of the characters with related species of the genus show that these strains represent three novel species of the genus Streptomyces. Therefore, the names Streptomyces tateyamensis sp. nov., Streptomyces haliclonae sp. nov. and Streptomyces marinus sp. nov. are proposed for strains Sp080513SC-30(T) (=NBRC 105048(T) =DSM 41969(T)), Sp080513SC-31(T) (=NBRC 105049(T) =DSM 41970(T)) and Sp080513GE-26(T) (=NBRC 105047(T) =DSM 41968(T)), respectively.