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

Tree species and moisture effects on soil sources of N2O: Quantifying contributions from nitrification and denitrification with O-18 isotopes

Nitrous oxide (N2O) is an important greenhouse gas and participates in the destruction of stratospheric ozone. Soil bacteria produce N2O through denitrification and nitrification, but these processes differ radically in substrate requirements and responses to the environment. Understanding the controls over N2O efflux from soils, and how N2O emissions may change with climate warming and altered precipitation, require quantifying the relative contributions from these groups of soil bacteria to the total N2O flux. Here we used ammonium nitrate (NH4NO3, including substrates for both processes) in which the nitrate has been enriched in the stable isotope of oxygen, O-18, to partition microbial sources of N2O, arguing that a molecule of N2O carrying the O-18 labeled will have been produced by denitrification. We compared the influences of six common tree species on the relative contributions of nitrification and denitrification to N2O flux from soils, using soils from the Siberian afforestation experiment. We also altered soil water content, to test whether denitrification becomes a dominant source of N2O when soil water content increases. Tree species altered the proportion of nitrifier and denitrifier-derived N2O. Wetter soils produced more N2O from denitrification, though the magnitude of this effect varied among tree species. This indicates that the roles of denitrification and nitrification vary with tree species, and, that tree species influence soil responses to increased water content

Stable isotope discrimination during soil denitrification: Production and consumption of nitrous oxide

Measuring the stable isotope composition of nitrous oxide ( N(2)O) evolved from soil could improve our understanding of the relative contributions of the main microbial processes ( nitrification and denitrification) responsible for N(2)O formation in soil. However, interpretation of the isotopic data in N(2)O is complicated by the lack of knowledge of fractionation parameters by different microbial processes responsible for N(2)O production and consumption. Here we report isotopic enrichment for both nitrogen and oxygen isotopes in two stages of denitrification, N(2)O production and N(2)O reduction. We found that during both N(2)O production and reduction, enrichments were higher for oxygen than nitrogen. For both elements, enrichments were larger for N(2)O production stage than for N(2)O reduction. During gross N(2)O production, the ratio of delta(18)O- to-delta(15)N differed between soils, ranging from 1.6 to 2.7. By contrast, during N(2)O reduction, we observed a constant ratio of delta(18)O- to-delta(15)N with a value near 2.5. If general, this ratio could be used to estimate the proportion of N(2)O being reduced in the soil before escaping into the atmosphere. Because N(2)O- reductase enriches N(2)O in both isotopes, the global reduction of N(2)O consumption by soil may contribute to the globally observed isotopic depletion of atmospheric N(2)O

Global change, nitrification, and denitrification: A review

We reviewed responses of nitrification, denitrification, and soil N2O efflux to elevated CO2, N availability, and temperature, based on published experimental results. We used meta-analysis to estimate the magnitude of response of soil N2O emissions, nitrifying enzyme activity (NEA), denitrifying enzyme activity (DEA), and net and gross nitrification across experiments. We found no significant overall effect of elevated CO2 on N2O fluxes. DEA and NEA significantly decreased at elevated CO2; however, gross nitrification was not modified by elevated CO2, and net nitrification increased. The negative overall response of DEA to elevated CO2 was associated with decreased soil [NO3-], suggesting that reduced availability of electron acceptors may dominate the responses of denitrification to elevated CO2. N addition significantly increased field and laboratory N2O emissions, together with gross and net nitrification, but the effect of N addition on field N2O efflux was not correlated to the amount of N added. The effects of elevated temperature on DEA, NEA, and net nitrification were not significant: The small number of studies available stress the need for more warming experiments in the field. While N addition had large effects on measurements of nitrification and denitrification, the effects of elevated CO2 were less pronounced and more variable, suggesting that increased N deposition is likely to affect belowground N cycling with a magnitude of change that is much larger than that caused by elevated CO2

Carbon protection and fire risk reduction: toward a full accounting of forest carbon offsets

Management of forests for carbon uptake is an important tool in the effort to slow the increase in atmospheric CO sub(2) and global warming. However, some current policies governing forest carbon credits actually promote avoidable CO sub(2) release and punish actions that would increase long-term carbon storage. In fire-prone forests, management that reduces the risk of catastrophic carbon release resulting from stand-replacing wild-fire is considered to be a CO sub(2) source, according to current accounting practices, even though such management may actually increase long-term carbon storage. Examining four of the largest wildfires in the US in 2002, we found that, for forest land that experienced catastrophic stand-replacing fire, prior thinning would have reduced CO sub(2) release from live tree biomass by as much as 98%. Altering carbon accounting practices for forests that have historically experienced frequent, low-severity fire could provide an incentive for forest managers to reduce the risk of catastrophic fire and associated large carbon release events

Effects of interactive global changes on methane uptake in an annual grassland.

The future size of the terrestrial methane (CH4) sink of upland soils remains uncertain, along with potential feedbacks to global warming. Much of the uncertainty lies in our lack of knowledge about potential interactive effects of multiple simultaneous global environmental changes. Field CH4 fluxes and laboratory soil CH4 consumption were measured five times during 3 consecutive years in a California annual grassland exposed to 8 years of the full factorial combination of ambient and elevated levels of precipitation, temperature, atmospheric CO2 concentration, and N deposition. Across all sampling dates and treatments, increased precipitation caused a 61% reduction in field CH4 uptake. However, this reduction depended quantitatively on other global change factors. Higher precipitation reduced CH4 uptake when temperature or N deposition (but not both) increased, and under elevated CO2 but only late in the growing season. Warming alone also decreased CH4 uptake early in the growing season, which was partly explained by a decrease in laboratory soil CH4 consumption. Atmospheric CH4 models likely need to incorporate nonadditive interactions, seasonal interactions, and interactions between methanotrophy and methanogenesis. Despite the complexity of interactions we observed in this multifactor experiment, the outcome agrees with results from single‐factor experiments: an increased terrestrial CH4 sink appears less likely than a reduced one

mRNA, rRNA and DNA Quantitative Stable Isotope Probing with H218O Indicates Use of Old rRNA among Soil Thaumarchaeota

RNA is considered to be a short-lived molecule, indicative of cellular metabolic activity, whereas DNA is thoughtto turn over more slowly because living cells do not always grow and divide. To explore differences in the ratesof synthesis of these nucleic acids, we used H218O quantitative stable isotope probing (qSIP) to measure theincorporation of18O into 16S rRNA, the 16S rDNA,amoAmRNA and theamoAgene of soil Thaumarchaeota.Incorporation of18O into the thaumarchaealamoAmRNA pool was faster than into the 16S rRNA pool,suggesting that Thaumarchaea were metabolically active while using rRNA molecules that were likely synthe-tized prior to H218O addition. Assimilation rates of18O into 16S rDNA andamoAgenes were similar, which wasexpected because both genes are present in the same thaumarchaeal genome. The Thaumarchaea had sig-nificantly higher rRNA to rDNA ratios than bacteria, though the18O isotopic signature of thaumarchaeal rRNAwas lower than that of bacterial rRNA, further suggesting preservation of old non-labeled rRNA. Through qSIP ofsoil with H218O, we showed that18O incorporation into thaumarchaeal nucleic acids was generally low, in-dicating slower turnover rates compared to bacteria, and potentially suggesting thaumarchaeal capability forpreservation and efficient reuse of biomolecules

Colonizing opportunistic pathogens (COPs): The beasts in all of us.

Colonizing opportunistic pathogens (COPs) are microbes that asymptomatically colonize the human body and, when the conditions are right, can cause infections. Their ability to persist indefinitely and to be transmitted without detection [1] gives COPs a unique epidemiology that warrants special consideration. There are examples of COPs among bacteria, fungi (e.g., Candida albicans [2]), protozoa (e.g., Blastocystis [3, 4]), and viruses (e.g., Rhinovirus [5]), but bacterial COPs are of particular relevance because of their major contribution to today’s antibiotic resistance crisis. The COPs include a long list of notorious bacteria that live double lives as passive stowaways and virulent foes. Some of the best-known COPs include Staphylococcus aureus, extraintestinal pathogenic Escherichia coli (ExPEC), Klebsiella pneumoniae, and Streptococcus pneumoniae (Table 1). Their capacity for benign coexistence with humans belies their alter egos that exact a heavy burden of human disease. For example, in the United States, ExPEC bloodstream infections kill as many as 40,000 people annually [6], but, ExPEC are also benign colonizers in the gastrointestinal tract [7]. Host factors, including age, sex, health status, anatomy, and behavior, all play profound roles in infection susceptibility and severity [8–10]. In particular, immunocompromised individuals are at excess risk for infections caused by diverse bacteria, including COPs [11, 12] and even commensals. Yet, health status is not the sole determinant of infection by COPs. For example, healthy women more frequently suffer from urinary tract infections than men because of anatomical differences, including shorter urethrae. Likewise, healthy children more commonly suffer from acute otitis media than adults due to their shorter, flatter eustachian tubes [13]

Antibiotic-resistant Escherichia Coli from Retail Poultry Meat with Different Antibiotic Use Claims

Background We sought to determine if the prevalence of antibiotic-resistant Escherichia coli differed across retail poultry products and among major production categories, including organic, “raised without antibiotics”, and conventional. Results We collected all available brands of retail chicken and turkey—including conventional, “raised without antibiotic”, and organic products—every two weeks from January to December 2012. In total, E. coli was recovered from 91% of 546 turkey products tested and 88% of 1367 chicken products tested. The proportion of samples contaminated with E. coli was similar across all three production categories. Resistance prevalence varied by meat type and was highest among E. coli isolates from turkey for the majority of antibiotics tested. In general, production category had little effect on resistance prevalence among E. coli isolates from chicken, although resistance to gentamicin and multidrug resistance did vary. In contrast, resistance prevalence was significantly higher for 6 of the antibiotics tested—and multidrug resistance—among isolates from conventional turkey products when compared to those labelled organic or “raised without antibiotics”. E. coli isolates from chicken varied strongly in resistance prevalence among different brands within each production category. Conclusion The high prevalence of resistance among E. coli isolates from conventionally-raised turkey meat suggests greater antimicrobial use in conventional turkey production as compared to “raised without antibiotics” and organic systems. However, among E. coli from chicken meat, resistance prevalence was more strongly linked to brand than to production category, which could be caused by brand-level differences during production and/or processing, including variations in antimicrobial use

Aligning ecology and markets in the forest carbon cycle

A forest carbon (C) offset is a quantifiable unit of C that is commonly developed at the local or regional project scale and is designed to counterbalance anthropogenic C emissions by sequestering C in trees. In cap-and-trade programs, forest offsets have market value if the sequestered C is additional (more than would have occurred in the absence of the project) and permanent (sequestered within the project boundary for a specified period of time). Local management and ecological context determine the rate of C sequestration, risk of loss, and hence the market value. An understanding of global C dynamics can inform policy but may not be able to effectively price an ecosystem service, such as C sequestration. Appropriate pricing requires the assistance of ecologists to assess C stock abundance and stability over spatial and temporal scales appropriate for the regional market. We use the risk that sequestered C will be emitted as a result of wildfire (reversal risk) to show how ecological context can influence market valuation in offset programs