Frank E. Löffler

Effects of elevated temperature on Dehalococcoides dechlorination performance and DNA and RNA biomarker abundance.

Coupling thermal treatment with microbial reductive dechlorination is a promising remedy for tetrachloroethene (PCE) and trichloroethene (TCE) contaminated source zones. Laboratory experiments evaluated Dehalococcoides (Dhc) dechlorination performance, viability, and biomarker gene (DNA) and transcript (mRNA) abundances during exposure to elevated temperatures. The PCE-dechlorinating consortia BDI and OW produced ethene when incubated at temperatures of 30 °C, but vinyl chloride (VC) accumulated when cultures were incubated at 35 or 40 °C. Cultures incubated at 40 °C for less than 49 days resumed VC dechlorination following cooling; however, incubation at 45 °C resulted in complete loss of dechlorination activity. Dhc 16S rRNA, bvcA, and vcrA gene abundances in cultures showing complete dechlorination to ethene at 30 °C exceeded those measured in cultures incubated at higher temperatures, consistent with observed dechlorination activities. Conversely, biomarker gene transcript abundances per cell in cultures incubated at 35 and 40 °C were generally at least one order-of-magnitude greater than those measured in ethene-producing cultures incubated at 30 °C. Even in cultures accumulating VC, transcription of the vcrA gene, which is implicated in VC-to-ethene dechlorination, was up-regulated. Temperature stress caused the up-regulation of Dhc reductive dehalogenase gene expression indicating that Dhc gene expression measurements should be interpreted cautiously as Dhc biomarker gene transcript abundances may not correlate with dechlorination activity.

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization

ABSTRACT The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for a better understanding of nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points during 1 year from two depths (0 to 5 and 20 to 30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty loam) with similar cropping histories. Although the microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural aquatic ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed a less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (are more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies. IMPORTANCE Even though the impact of agricultural management on the microbial community structure has been recognized, an understanding of the dynamics of individual microbial populations and what functions each population carries are limited. Yet, this information is important for a better understanding of nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here, we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic than their marine counterparts previously studied.

Release of Electron Donors during Thermal Treatment of Soils

Thermal treatment of soil and groundwater may provide an in situ source of soluble organic compounds and hydrogen (H2) that could stimulate microbial reductive dechlorination (MRD) at sites impacted by chlorinated solvents. The objectives of this study were to identify and quantify the release of electron donors and fermentable precursors during soil heating and to estimate availability of these compounds following thermal treatment. Fourteen solid materials containing <0.01 to 63.81 wt % organic carbon (OC) were incubated at 30, 60, or 90 °C for up to 180 d, leading to the release of direct electron donors (i.e., H2 and acetate) and fermentable volatile fatty acids (VFAs). Total VFA release ranged from 5 ± 0 × 10-9 carbon per gram solid (mol C/gs) during 30 °C incubation of quartz sand to 820 ± 50 × 10-6 mol C/gs during 90 °C incubation of humic acid, and was positively impacted by incubation time, temperature, and solid-phase OC content. H2 gas was detected at a maximum of 180 ± 50 × 10-9 mol H2/gs, accounting for less than 0.3% of reducing equivalents associated with VFAs released under the same conditions. These findings will allow for more reliable prediction of substrate release during thermal treatment, supporting the implementation of coupled thermal and biological remediation strategies.