Stable Carbon Isotope Fractionation in Chlorinated Ethene Degradation by Bacteria Expressing Three Toluene Oxygenases

One difficulty in using bioremediation at a contaminated site is demonstrating that biodegradation is actually occurring in situ. The stable isotope composition of contaminants may help with this, since they can serve as an indicator of biological activity. To use this approach it is necessary to establish how a particular biodegradation pathway affects the isotopic composition of a contaminant. This study examined bacterial strains expressing three aerobic enzymes for their effect on the 13C/12C ratio when degrading both trichloroethene (TCE) and cis-1,2-dichloroethene (c-DCE): toluene 3-monoxygenase, toluene 4-monooxygenase, and toluene 2,3-dioxygenase. We found no significant differences in fractionation among the three enzymes for either compound. Aerobic degradation of c-DCE occurred with low fractionation producing δ13C enrichment factors of −0.9 ± 0.5 to −1.2 ± 0.5, in contrast to reported anaerobic degradation δ13C enrichment factors of −14.1 to −20.4‰. Aerobic degradation of TCE resulted in δ13C enrichment factors of −11.6 ± 4.1 to −14.7 ± 3.0‰ which overlap reported δ13C enrichment factors for anaerobic TCE degradation of −2.5 to −13.8‰. The data from this study suggest that stable isotopes could serve as a diagnostic for detecting aerobic biodegradation of TCE by toluene oxygenases at contaminated sites

Reconstructing each cell’s genome within complex microbial communities - dream or reality?

As the vast majority of microorganisms have yet to be cultivated in a laboratory setting, access to their genetic makeup has largely been limited to cultivation-independent methods. These methods, namely metagenomics and more recently single-cell genomics, have become cornerstones for microbial ecology and environmental microbiology. One ultimate goal is the recovery of genome sequences from each cell within an environment to move towards a better understanding of community metabolic potential and to provide substrate for experimental work. As single-cell sequencing has the ability to decipher all sequence information contained in an individual cell, this method holds great promise in tackling such challenge. Methodological limitations and inherent biases however do exist, which will be discussed here as based on environmental and benchmark data, to assess on how far we are from reaching this goal

Geochemistry and Mixing Drive the Spatial Distribution of Free-living Archaea and Bacteria in Yellowstone Lake

Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8 µm, 0.8-3.0 µm, and 3.0-20 µm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 & V2 regions of 16S rRNA genes. Nonmetric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the Lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO42-, O2 and metals were likely the major drivers for microbial population structures, however mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (>3 µm) and contained higher predicted OTU richness and microbial diversities (genus level) than free-living ones (< 0.8 µm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur