Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon. Three different soil types from the Canadian high Arctic were sampled at two depths within the active layer of soil and at two sampling dates (winter and summer conditions), for a total of 20 samples.
Project description:Transcriptomic sequencing was performed to obtain the key functional genes involved in the adaptation of oxidative stress induced by hydrogen peroxide (H2O2) in the Arctic bacterium Pseudoalteromonas sp. A2. Exposure to 1 mmol/L H2O2 resulted in large alterations of the transcriptome profile, including significant upregulation of 109 genes and significant downregulation of 174 genes. Functional classification of differentially expressed genes revealed that most of genes affiliated with biological adhesion, negative regulation of biological process, enzyme regulator activity, protein binding transcription factor activity and structural molecular activity were upregulated, and most of genes affiliated with multicellular organismal process and extracellular region were downregulated. It was notably that fifteen genes affiliated with flagella and four genes affiliated with heat shock proteins were significantly upregulated. Meanwhile, nine genes affiliated with cytochrome and cytochrome oxidase, and five genes affiliated with TonB-dependent receptor, were significantly downregulated. However, eighteen genes with antioxidant activity categorized by GO analysis showed differential expressions. This overall survey of transcriptome and oxidative stress-relevant genes can contribute to understand the adaptive mechanism of Arctic bacteria. five significant upregulated genes and five significant downregulated genes were selected using qRT-PCR to cinduct the oxidative stress. overall survey of transcriptomic sequencing by RNA-Seq of the Pseudoalteromonas sp. A2, an isolate from seawater with high activity against H2O2
Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.