Bioconversion of coal: New insights from a core flooding study

A pressurized core flooding experiment was performed to better understand in situ coal bioconversion processes. The core flooding experiment was conducted using a biaxial core holder packed with subbituminous coal particles (250-150 μm grain size) obtained from the Highvale mine in Alberta, Canada. The coal pack was inoculated with a methanogenic microbial culture enriched from coal and was continuously flooded with mineral salt medium and an organic carbon/nitrogen nutrient supplement (tryptone). The changes in the physical properties of the coal pack during the core flooding suggested coal bioconversion to methane under the experimental conditions. Colonization and bioconversion of coal by microbes was evident from the change in core permeability and presence of metabolites and gas (CH4 and CO 2) in the effluent. A total of 1.52 μmol of CH4 was produced per gram of coal during the 90 days experiment at 22 °C. Signature metabolites consistent with anaerobic biodegradation of hydrocarbons, e.g., carboxylic acids, were identified in effluent samples throughout incubation. The transient nature of metabolites in effluent samples supports fermentation of coal constituents and nutrient supplement to simple molecules such as acetic acid, which served as a substrate for methanogenesis during the bioconversion process. Accumulation of carboxylic acids such as succinic acid in the effluent also demonstrates that the coal bioconversion process may be used for extraction of other value-added products apart from CH4 generation. Importantly, results presented here suggest that coal bioconversion by biostimulation under reservoir conditions is a scalable technology with potential for energy generation and for overall reduction of greenhouse gas emissions. This journal i

METAGENassist: A comprehensive web server for comparative metagenomics

With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative metagenomics. Comparative metagenomics involves the comparison of bacterial populations between different environmental samples, different culture conditions or different microbial hosts. However, in order to do comparative metagenomics, one typically requires a sophisticated knowledge of multivariate statistics and/or advanced software programming skills. To make comparative metagenomics more accessible to microbiologists, we have developed a freely accessible, easy-to-use web server for comparative metagenomic analysis called METAGENassist. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data. Metadata concerning environmental, culture, or host conditions can also be uploaded. During the data upload process, METAGENassist also performs an automated taxonomic-to-phenotypic mapping. Phenotypic information covering nearly 20 functional categories such as GC content, genome size, oxygen requirements, energy sources and preferred temperature range is automatically generated from the taxonomic input data. Using this phenotypically enriched data, users can then perform a variety of multivariate and univariate data analyses including fold change analysis, t-tests, PCA, PLS-DA, clustering and classification. To facilitate data processing, users are guided through a step-by-step analysis workflow using a variety of menus, information hyperlinks and check boxes. METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca. \ua9 2012 The Author(s).Peer reviewed: YesNRC publication: Ye

A global perspective on bacterial diversity in the terrestrial deep subsurface.

While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling

A global perspective on bacterial diversity in the terrestrial deep subsurface

While recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12–20 % of Earth’s biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling