Project description:The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters. The abundance of nosZ genes, as estimated by quantitative PCR, was highest in the agricultural soils and lowest in surface ocean waters.
Project description:In this study, microbial communities from triplicate leach-bed anaerobic bioreactors digesting grass were analysed. Each reactor comprised two microbial fractions, one immobilized on grass (biofilm) and the other in a planktonic state present in the leachate. Microbial communities from the two fractions were systematically investigated for community composition and function. This was carried out using DNA, RNA and protein co-extraction. The microbial structure of each fraction was examined using 16S rRNA deep sequencing, while the active members of the consortia were identified using the same approach on cDNA generated from co-extracted RNA samples. Microbial function was investigated using a metaproteomic workflow combining SDS-PAGE and LC-MS/MS analysis.
Project description:Known as “The Oriental Botanic Garden” and the natural gene bank of biological species, Shennongjia is one of the most biologically diverse areas in China and a member of UNESCO's World Network of Biosphere Reserves. The macro-organism resources of shennongjia have been deeply explored. However, the microbial community structure was scarcely detected. In this study, we aim to detedect the microbial community along six sites of Shennonajia Mountain and explore the major controlling factor in shaping microbial community with a microarray-based metagenomics tool named GeoChip 4.2.
Project description:Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered “generalist” and “specialist” archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 11-29% of the abundant NRE archetypes. Archetypes found in a particular site, “specialists”, were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe2+. A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H2S, respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among denitrifying communities and supports the essential role of individual community members in overall ecosystem function.
