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Abstracts of Recent Publications
Abstracts 1 2 3 4 5 6 

001-Asha Rani , Shalini Porwal , Rakesh Sharma , Atya Kapley , Hemant, Purohit ,Vipin Chandra Kalia. Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi – 110007, India. Assessment of microbial diversity in effluent treatment plants by culture dependent and cul ture independent approaches. Bioresource Technology, 2008, 1 – 10.

Microbial community structure of two distinct effluent treatment plants (ETPs) of pesticide and pharmaceutical industries were assessed and defined by (i) culture dependent and culture independent approaches on the basis of 16S rRNA gene sequencing, and (ii)diversity index analysis – operational taxonomic units (OTUs). A total of 38 and 44 bacterial OTUs having 85–99% similarity with the closest match in the database were detected among pharmaceutical and pesticide sludge samples, respectively. Fifty percent of the OTUs were related to uncultured bacteria. These OTUs had a Shannon diversity index value of 2.09–2.33 for culturables and in the range of 3.25–3.38 for unculturables. The high species evenness values of 0.86 and 0.95 indicated the vastness of microbial diversity retrieved by these approaches. The dominant cultured bacteria indicative of microbial diversity in functional ETPs were Alcaligenes, Bacillus and Pseudomonas. Brevundimonas, Citrobacter, Pandoraea and Stenotrophomonas were specific to pesticide ETP, where as Agrobacterium, Brevibacterium, Micrococcus, Microbacterium, Paracoccus and Rhodococcus were specific to pharmaceutical ETP. These microbes can thus be maintained and exploited for efficient functioning and maintenance of ETPs.

Keywords: Effluent; Metagenomics; Microbial diversity; Unculturable; 16S rRNA gene.


002-Lisa M. Gieg, Kathleen E. Duncan, and Joseph M. Suflita. Department of Botany and Microbiology, University of Oklahoma, 770 Van Vleet Oval, Rm. 135, Norman, OK 73019. Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas. Applied and Environmental Microbiology, 74, 2008, 3022-3029.

World requirements for fossil energy are expected to grow by more than 50% within the next25 years, despite advances in alternative technologies. Since conventional production methods retrieve only about one-third of the oil in place, either large new fields or innovative strategies for recovering energy resources from existing fields are needed to meet the burgeoning demand. The anaerobic biodegradation of n-alkanes to methane gas has now been documented in a few studies, and it was speculated that this process might be useful for recovering energy from existing petroleum reservoirs. We found that residual oil entrained in a marginal sandstone reservoir core could be converted to methane, a key component of natural gas, by an oil-degrading methanogenic consortium. Methane production required inoculation, and rates ranged from 0.15 to 0.40 mol/day/g core (or 11 to 31 ìmol/day/g oil), with yields of up to 3 mmol CH4/g residual oil. Concomitant alterations in the hydrocarbon profile of the oil-bearing core revealed that alkanes were preferentially metabolized. The consortium was found to produce comparable amounts of methane in the absence or presence of sulfate as an alternate electron acceptor. Cloning and sequencing exercises revealed that the inoculum comprised sulfate-reducing, syntrophic, and fermentative bacteria acting in concert with aceticlastic and hydrogenotrophic methanogens. Collectively, the cells generated methane from a variety of petroliferous rocks. Such microbe-based methane production holds promise for producing a clean-burning and efficient form of energy from underutilized hydrocarbon-bearing resources.

Keywords:Residual Oi l , Natural Gas, biodegradation, alkanes, methane, Microbial Conversion.


003- R. Vílchez, C. Pozo, M. A. Gómez, B. Rodelas and J. González-López. Helmholtz Center for Infection Research, Department of Cell Biology and Immunology, Inhoffenstrabe 7, D-38124 Braunschweig, Germany. Dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment. Microbiology, 153, 2007, 325-337.

The structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. A laboratory-scale submerged fixed biofilter was fed with groundwater(2.3 l h-1) artificially polluted with Cu(II) (15 mg l-1) and amended with sucrose (150 mg l-1) as carbon source. Between 73 and 90% of the Cu(II) was removed from water during long-term operation (over 200 days). The biofilm was a complex ecosystem, consisting of eukaryotic and prokaryotic micro-organisms. Scanning electron microscopy revealed marked structural changes in the biofilm induced by Cu(II), compared to the biofilm grown in absence of the heavy metal. Analysis of cell-bound extracellular polymeric substances (EPS) demonstrated a significant modification of the composition of cell envelopes in response to Cu (II). Transmission electron microscopy and energydispersive X-ray microanalysis (EDX) showed that copper bioaccumulated in the EPS matrix by becoming bound to phosphates and/or silicates, where as copper accu mulated only intracytoplasmically in cells of eukaryotic microbes. Cu(II) also decreased sucrose consumption, ATP content and alkaline phosphatase activity of the biofilm. A detailed study of the bacterial community composition was conducted by 16S rRNA-based temperature gradient gel electrophoresis (TGGE) profiling, which showed spatial and temporal stability of the species diversity of copper-exposed biofilms during biofilter operation. PCR reamplification and sequencing of 14 TGGE bands showed the prevalence of alphaproteobacteria, with most sequences (78%) affiliated to the Sphingomonadaceae. The major cultivable colony type in plate counts of the copper-exposed biofilm was also identified as that of Sphingomonas sp. These data confirm a major role of these organisms in the composition of the Cu (II)-removing community.

Keywords:Groundwater treatment, biological activity, biofilm, eukaryotic microbes, rRNA, PCR, alkaline.


004-Catherine A. Lozupone and Rob Knight. Departments of Molecular, Cellular, and Developmental Biology and Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309. Global patterns in bacterial diversity. PNAS, 104, 2007, 11436-11440.

Microbes are difficult to culture. Consequently, the primary source of information about a fundamental evolutionary topic, life’s diversity, is the environmental distribution of gene sequences. We report the most comprehensive analysis of the environmental distribution of bacteria to date, based on 21,752 16S rRNA sequencescompiled from 111 studies of diverse physical environments. We clustered the samples based on similarities in the phylogenetic lineages that they contain and found that, surprisingly, the major environmental determinant of microbial community composition is salinity rather than extremes of temperature, pH, or other physical and chemical factors represented in our samples. We find that sediments are more phylogenetically diverse than any other environment type. Surprisingly, soil, which has high species-level diversity, has below-average phylogenetic diversity. This work provides a framework for understanding the impact of environmental factors on bacterial evolution and for the direction of future sequencing efforts to discover new lineages

Keywords: environmental distribution, microbial ecology, phylogenetic diversity, UniFrac, bacterial diversity.


005-Daisuke Inoue, Shoji Hara, Mari Kashihara, Yusaku Murai, Erica Danzl, Kazunari Sei,Shinji Tsunoi, Masanori Fujita, and Michihiko Ike. Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1Yamadaoka, Suita, Osaka 565-0871, Japan. Degradation of Bis(4- Hydroxyphenyl)Methane (Bisphenol F) by Sphingobium yanoikuyae Strain FM-2 Isolated from River Water. Applied and Environmental Microbiology, 74, 2008, 352–358.

Three bacteria capable of utilizing bis(4- hydroxyphenyl)methane (bisphenol F [BPF]) as the sole carbon source were isolated from river water, and they all belong to the family Sphingomonadaceae. One of the isolates, designated Sphingobium yanoikuyae strain FM-2, at an initial cell density of 0.01 (optical density at 600 nm) completely degraded 0.5 mM BPF within 9 h without any lag period under inductive conditions. Degradation assays of various bisphenols revealed that the BPF-metabolizing system of strain FM-2 was effective only on the limited range of bisphenols consisting of two phenolic rings joined together through a bridging carbon without any methyl substitution on the rings or on the bridging structure. A BPF biodegradation pathway was proposed on the basis of metabolite production patterns and identification of the metabolites. The initial step of BPF biodegradation involves hydroxylation of the bridging carbon to form bis(4-hydroxyphenyl) methanol, followed by oxidation to 4,4- di hydroxybenzophenone. T h e 4 , 4 - dihydroxybenzophenone appears to be furtheroxidized by the Baeyer-Villiger reaction to 4- hydroxyphenyl 4-hydroxybenzoate, which is then cleaved by oxidation to form 4-hydroxybenzoate and 1,4-hydroquinone. Both of the resultant simple aromatic compounds are mineralized.

Keywords:Microbial Conversion, alkanes, methane, Bioenergy Production, Residual Oil, Natural Gas.


006-Kathryn A. Harrison, Roland Bol, Richard D. Bardgett. Soil and Ecosystem Ecology Laboratory, Institute of Environmental and Natural Sciences, Lancaster University, Lancaster, LA1 4YQ, UK. Do plant species with different growth strategies vary in their ability to compete with soil microbes for chemical forms of nitrogen? Soil Biology & Biochemistry, 40, 2008, 228–237.

We used dual labelled stable isotope (13c and 15N) techniques to examine how grassland plant species with different growth strategies vary in their ability to compete with soil microbes for different chemical forms of nitrogen (N), both inorganic and organic. We also tested whether some plant species might avoid competition by preferentially using different chemical forms of N than microbes. This was tested in a pot experiment where monocultures of five co-existing grassland species, namely the grasses Agrostis capillaris, Anthoxanthum odoratum, Nardus stricta, Deschampsia flexuosa and the herb Rumex acetosella, were grown in field soil from an acid semi-natural temperate grassland. Our data show that grassland plant species with different growth strategies are able to compete effectively with soil microbes for most N forms presented to them, including inorganic N and amino acids of varying complexity. Contrary to what has been found in strongly N limited ecosystems, we did not detect any differential uptake of N on the basis of chemical form, other than that shoot tissue of fast-growing plant species was more enriched in 15 from N ammonium-nitrate and glycine, than from more complex amino acids. Shoot tissue of slowgrowing species was equally enriched in 15N from all these N forms. However, all species tested, least preferred the most complex amino acid phenylalanine, which was preferentially used by soil microbes. We also found that while fastgrowing plants took up more of the added N forms than slow-growing species, this variation was not related to differences in the ability of plants tocompete with microbes for N forms, as hypothesised. On the contrary, we detected no difference in microbial biomass or microbial uptake of 15N between fast and slow-growing plant species, suggesting that plant traits that regulate nutrient capture, as opposed to plant species-specific interactions with soil microbes, are the main factor controlling variation in uptake of N by grassland plant species. Overall, our data provide insights into the interactions between plants and soil microbes that influence plant nitrogen use in grassland ecosystems.

Keywords: Amino acids; Grassland; Organic nitrogen; Inorganic nitrogen; Microbial biomass; Plantmicrobial competition; Stable isotopes; Growth strategies; Nitrogen.


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