Effects of electron acceptors and donors on transformation of tetrachloromethane by Shewanella putrefaciens MR-1

Transformation of chlorinated aliphatic compounds was examined in Shewanella putrefaciens strain MR-1, an obligately respiring facultative anaerobe. Under anaerobic conditions, MR-1 has been shown to transform tetrachloromethane to trichloromethane (24%), CO 2 (7%), cell-bound material (50%) and unidentified nonvolatile products (4%). The highest rate and extent of transformation were observed with MR-1 cells grown under iron(III)-respiring conditions. Lactate, formate and hydrogen were the most effective electron donors. Tetrachloromethane was not degraded in the presence of oxygen. Transformation of other chlorinated methanes and ethenes was not observed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73742/1/j.1574-6968.1994.tb07126.x.pd

Dechlorination of 2,3,5,6-tetrachlorobiphenyl by a phototrophic enrichment culture

A phototrophic enrichment culture, using acetate as carbon source, reductively dechlorinated 2,3,5,6-tetrachlorobiphenyl. ortho chlorines were removed preferentially over meta chlorines. Tri- and dichlorobiphenyls were the major products. During 14 months incubation, chlorine was removed from 58% of the target molecules; 19% of the total chlorines were removed. Dechlorination did not occur in a control culture incubated in the dark.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29945/1/0000303.pd

Observations of stem water storage in trees of opposing hydraulic strategies

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/116368/1/ecs2201569165.pd

Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms

Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction of prokaryote homologous genes families detected 151 genes (13.3%) of foreign origin in the R. solanacearum genome and tentatively identified their bacterial origin. These putative transfers were analyzed in comparison to experimental transformation tests involving 18 different genomic DNA positions in the genome as sites for homologous or homeologous recombination. Significant transformation frequency differences were observed among these positions tested regardless of the overall genomic divergence of the R. solanacearum strains tested as recipients. The genomic positions containing the putative exogenous DNA were not systematically transformed at the highest frequencies. The two genomic “hot spots”, which contain recA and mutS genes, exhibited transformation frequencies from 2 to more than 4 orders of magnitude higher than positions associated with other genes depending on the recipient strain. These results support the notion that the bacterial cell is equipped with active mechanisms to modulate acquisition of new DNA in different genomic positions. Bio-informatics study correlated recombination “hot-spots” to the presence of Chi-like signature sequences with which recombination might be preferentially initiated. The fundamental role of HGT is certainly not limited to the critical impact that the very rare foreign genes acquired mainly by chance can have on the bacterial adaptation potential. The frequency to which HGT with homologous and homeologous DNA happens in the environment might have led the bacteria to hijack DNA repair mechanisms in order to generate genetic diversity without losing too much genomic stability

Over winter microbial processes in a Svalbard snow pack:an experimental approach

International audienceSnow packs cover large expanses of Earth’s land surface, making them integral components of the cryosphere in terms of past climate and atmospheric proxies, surface albedo regulators, insulators for other Arctic environments and habitats for diverse microbial communities such as algae, bacteria and fungi. Yet, most of our current understanding of snow pack environments, specifically microbial activity and community interaction, is limited to the main microbial growing season during spring ablation. At present, little is known about microbial activity and its influence on nutrient cycling during the subfreezing temperatures and 24-h darkness of the polar winter. Here, we examined microbial dynamics in a simulated cold (−5°C), dark snow pack to determine polar winter season microbial activity and its dependence on critical nutrients. Snow collected from Ny-Ålesund, Svalbard was incubated in the dark over a 5-week period with four different nutrient additions, including glacial mineral particles, dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and a combined treatment of DIN plus DIP. Data indicate a consumption of dissolved inorganic nutrients, particularly DIN, by heterotrophic communities, suggesting a potential nitrogen limitation, contradictory to phosphorus limitations found in most aquatic environments. 16S amplicon sequencing also reveal a clear difference in microbial community composition in the particulate mineral treatment compared to dissolved nutrient treatments and controls, suggesting that certain species of heterotrophs living within the snow pack are more likely to associate with particulates. Particulate phosphorus analyses indicate a potential ability of heterotrophic communities to access particulate sources of phosphorous, possibly explaining the lack of phosphorus limitation. These findings have importance for understanding microbial activity during the polar winter season and its potential influences on the abundance and bioavailability of nutrients released to surface ice and downstream environments during the ablation season

Biodegradation of monoaromatic hydrocarbons in aquifer columns amended with hydrogen peroxide and nitrate

The ability of indigenous microorganisms to degrade benzene, toluene, ethylbenzene and xylenes (BTEX) in laboratory scale flow-through aquifer columns was tested separately with hydrogen peroxide (110 mg/l) and nitrate (330 mg/l as NO3-) amendments to air-saturated influent nutrient solution. The continuous removal of individual components from all columns relative to the sterile controls provided evidence for biodegradation. In the presence of hydrogen peroxide, the indigeneous microorganisms degraded benzene and toluene ( > 95%), meta- plus para-xylene (80%) and ortho-xylene (70%). Nitrate addition resulted in 90% removal of toluene and 25% removal of ortho-xylene. However, benzene, ethylbenzene, meta- and para-xylene concentrations were not significantly reduced after 42 days of operation. Following this experiment, low dissolved oxygen ( 90%), and more than 25% of the benzene, 40% of the ethylbenzene, 50% of the meta- plus para-xylenes and 60% of the ortho-xylene were removed after several months of operation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30890/1/0000559.pd

Zebrafish orthologs of human muscular dystrophy genes

BACKGROUND: Human muscular dystrophies are a heterogeneous group of genetic disorders which cause decreased muscle strength and often result in premature death. There is no known cure for muscular dystrophy, nor have all causative genes been identified. Recent work in the small vertebrate zebrafish Danio rerio suggests that mutation or misregulation of zebrafish dystrophy orthologs can also cause muscular degeneration phenotypes in fish. To aid in the identification of new causative genes, this study identifies and maps zebrafish orthologs for all known human muscular dystrophy genes. RESULTS: Zebrafish sequence databases were queried for transcripts orthologous to human dystrophy-causing genes, identifying transcripts for 28 out of 29 genes of interest. In addition, the genomic locations of all 29 genes have been found, allowing rapid candidate gene discovery during genetic mapping of zebrafish dystrophy mutants. 19 genes show conservation of syntenic relationships with humans and at least two genes appear to be duplicated in zebrafish. Significant sequence coverage on one or more BAC clone(s) was also identified for 24 of the genes to provide better local sequence information and easy updating of genomic locations as the zebrafish genome assembly continues to evolve. CONCLUSION: This resource supports zebrafish as a dystrophy model, suggesting maintenance of all known dystrophy-associated genes in the zebrafish genome. Coupled with the ability to conduct genetic screens and small molecule screens, zebrafish are thus an attractive model organism for isolating new dystrophy-causing genes/pathways and for use in high-throughput therapeutic discovery

Contrasting strategies of hydraulic control in two codominant temperate tree species

Biophysical controls on plant water status exist at the leaf, stem, and root levels. Therefore, we pose that hydraulic strategy is a combination of traits governing water use at each of these three levels. We studied sap flux, stem water storage, stomatal conductance, photosynthesis, and growth of red oaks (Quercus rubra) and red maples (Acer rubrum). These species differ in stomatal hydraulic strategy and xylem architecture and may root at different depths. Stable isotope analysis of xylem water was used to identify root water uptake depth. Oaks were shown to access a deeper water source than maples. During non‐limiting soil moisture conditions, transpiration was greater in maples than in oaks. However, during a soil dry down, transpiration and stem water storage decreased by more than 80% and 28% in maples but only by 31% and 1% in oaks. We suggest that the preferential use of deep water by red oaks allows the species to continue transpiration and growth during soil water limitations. In this case, deeper roots may provide a buffer against drought‐induced mortality. Using 14 years of growth data, we show that maple growth correlates with mean annual soil moisture at 30 cm but oak growth does not. The observed responses of oak and maple to drought were not able to be explained by leaf and xylem physiology alone. We employed the Finite‐difference Ecosystem‐scale Tree Crown Hydrodynamics model version 2 plant hydrodynamics model to demonstrate the influence of root, stem, and leaf controls on tree‐level transpiration. We conclude that all three levels of hydraulic traits are required to define hydraulic strategy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136732/1/eco1815_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136732/2/eco1815.pd

Species‐specific transpiration responses to intermediate disturbance in a northern hardwood forest

Intermediate disturbances shape forest structure and composition, which may in turn alter carbon, nitrogen, and water cycling. We used a large‐scale experiment in a forest in northern lower Michigan where we prescribed an intermediate disturbance by stem girdling all canopy‐dominant early successional trees to simulate an accelerated age‐related senescence associated with natural succession. Using 3 years of eddy covariance and sap flux measurements in the disturbed area and an adjacent control plot, we analyzed disturbance‐induced changes to plot level and species‐specific transpiration and stomatal conductance. We found transpiration to be ~15% lower in disturbed plots than in unmanipulated control plots. However, species‐specific responses to changes in microclimate varied. While red oak and white pine showed increases in stomatal conductance during postdisturbance (62.5 and 132.2%, respectively), red maple reduced stomatal conductance by 36.8%. We used the hysteresis between sap flux and vapor pressure deficit to quantify diurnal hydraulic stress incurred by each species in both plots. Red oak, a ring porous anisohydric species, demonstrated the largest mean relative hysteresis, while red maple, bigtooth aspen, and paper birch, all diffuse porous species, had the lowest relative hysteresis. We employed the Penman‐Monteith model for LE to demonstrate that these species‐specific responses to disturbance are not well captured using current modeling strategies and that accounting for changes to leaf area index and plot microclimate are insufficient to fully describe the effects of disturbance on transpiration.Key PointsPlot level scaling of evaporation from sap flux evaluated with eddy fluxDisturbance changes intradaily transpiration dynamicsHydraulic strategy causes species‐specific transpiration differencesPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110637/1/jgrg20315.pd