Benzo(a)pyrene degradation and microbial community responses in composted soil

Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation

Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ∼20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols

Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols

An Assessment of Climate Induced Increase in Soil Water Availability for Soil Bacterial Communities Exposed to Long-Term Differential Phosphorus Fertilization

The fate of future food productivity depends primarily upon the health of soil used for cultivation. For Atlantic Europe, increased precipitation is predicted during both winter and summer months. Interactions between climate change and the fertilization of land used for agriculture are therefore vital to understand. This is particularly relevant for inorganic phosphorus (P) fertilization, which already suffers from resource and sustainability issues. The soil microbiota are a key indicator of soil health and their functioning is critical to plant productivity, playing an important role in nutrient acquisition, particularly when plant available nutrients are limited. A multifactorial, mesocosm study was established to assess the effects of increased soil water availability and inorganic P fertilization, on spring wheat biomass, soil enzymatic activity (dehydrogenase and acid phosphomonoesterase) and soil bacterial community assemblages. Our results highlight the significance of the spring wheat rhizosphere in shaping soil bacterial community assemblages and specific taxa under a moderate soil water content (60%), which was diminished under a higher level of soil water availability (80%). In addition, an interaction between soil water availability and plant presence overrode a long-term bacterial sensitivity to inorganic P fertilization. Together this may have implications for developing sustainable P mobilization through the use of the soil microbiota in future. Spring wheat biomass grown under the higher soil water regime (80%) was reduced compared to the constant water regime (60%) and a reduction in yield could be exacerbated in the future when grown in cultivated soil that have been fertilized with inorganic P. The potential feedback mechanisms for this need now need exploration to understand how future management of crop productivity may be impacted.</p

Physical Conditions of Accreting Gas in T Tauri Star Systems

We present results from a low resolution (R~300) near-infrared spectroscopic variability survey of actively accreting T Tauri stars (TTS) in the Taurus-Auriga star forming region. Paschen and Brackett series H I recombination lines were detected in 73 spectra of 15 classical T Tauri systems. The values of the Pan/PaB, Brn/BrG, and BrG/Pan H I line ratios for all observations exhibit a scatter of < 20% about the weighted mean, not only from source to source, but also for epoch-to-epoch variations in the same source. A representative or `global' value was determined for each ratio in both the Paschen and Brackett series as well as the BrG/Pan line ratios. A comparison of observed line ratio values was made to those predicted by the temperature and electron density dependent models of Case B hydrogen recombination line theory. The measured line ratios are statistically well-fit by a tightly constrained range of temperatures (T < 2000 K) and electron densities 1e9 < n_e < 1e10 cm^-3. A comparison of the observed line ratio values to the values predicted by the optically thick and thin local thermodynamic equilibrium cases rules out these conditions for the emitting H I gas. Therefore, the emission is consistent with having an origin in a non-LTE recombining gas. While the range of electron densities is consistent with the gas densities predicted by existing magnetospheric accretion models, the temperature range constrained by the Case B comparison is considerably lower than that expected for accreting gas. The cooler gas temperatures will require a non-thermal excitation process (e.g., coronal/accretion-related X-rays and UV photons) to power the observed line emission.Comment: 12 pages, emulateapj format, Accepted for publication in Ap

Spitzer IRS Observations of the Galactic Center: Shocked Gas in the Radio Arc Bubble

We present Spitzer IRS spectra (R ~600, 10 - 38 micron) of 38 positions in the Galactic Center (GC), all at the same Galactic longitude and spanning plus/minus 0.3 degrees in latitude. Our positions include the Arches Cluster, the Arched Filaments, regions near the Quintuplet Cluster, the ``Bubble'' lying along the same line-of-sight as the molecular cloud G0.11-0.11, and the diffuse interstellar gas along the line-of-sight at higher Galactic latitudes. From measurements of the [O IV], [Ne II], [Ne III], [Si II], [S III], [S IV], [Fe II], [Fe III], and H_2 S(0), S(1), and S(2) lines we determine the gas excitation and ionic abundance ratios. The Ne/H and S/H abundance ratios are ~ 1.6 times that of the Orion Nebula. The main source of excitation is photoionization, with the Arches Cluster ionizing the Arched Filaments and the Quintuplet Cluster ionizing the gas nearby and at lower Galactic latitudes including the far side of the Bubble. In addition, strong shocks ionize gas to O^{+3} and destroy dust grains, releasing iron into the gas phase (Fe/H ~ 1.3 times 10^{-6} in the Arched Filaments and Fe/H ~ 8.8 times 10^{-6} in the Bubble). The shock effects are particularly noticeable in the center of the Bubble, but O$^{+3}$ is present in all positions. We suggest that the shocks are due to the winds from the Quintuplet Cluster Wolf-Rayet stars. On the other hand, the H_2 line ratios can be explained with multi-component models of warm molecular gas in photodissociation regions without the need for H_2 production in shocks.Comment: 51 pages, 17 figures To be published in the Astrophysical Journa

Soil bacterial community structure and functional responses across a long-term mineral phosphorus (Pi) fertilisation gradient differ in grazed and cut grasslands

peer-reviewedGrasslands form a significant proportion of land used across the globe and future management is important. The objective of this study was to compare the long-term impact of inorganic phosphorus (Pi) fertilisation rates (P0, P15 and P30 ha−1 yr−1) under two grass management trials (grazed vs. cut and removed) on soil physicochemical properties, microbial biomass, phosphomonoesterase activity, bacterial community structure and abundance of a phosphorus (P) mineralising gene (phoD). Under grazing, microbial biomass and soil phosphorus concentrations (total and Pi) generally increased with Pi fertilisation rate, accompanied by significant differences in bacterial community structure between unfertilised (P0) and P30 soil. At the cut and removed site, although Pi was significantly greater in P30 soil, P concentrations (total and Pi) did not increase to the same extent as for grazing, with microbial biomass and bacterial community structures unresponsive to Pi fertilisation. Despite differences in soil P concentrations (total and Pi) and microbial biomass between sites, the abundance of bacterial phoD increased with increasing soil Pi across both sites, while phosphomonoesterase activity decreased. Amplicon sequencing revealed Acidobacteria were the dominant bacterial phylum across both grasslands, but significant differences in relative abundances of bacterial genera were detected at the grazed site only. The bacterial genera Gp6 and Gp16 increased significantly with Pi fertilisation under grazing. Conversely, Bradyrhizobium as well as unclassified genus-type groups belonging to Actinobacteria and Acidimicrobiales significantly decreased with Pi fertilisation, suggesting potential roles in P mobilisation when soil Pi concentrations are low. This study highlights the importance of long-term Pi fertilisation rates and aboveground vegetation removal in shaping soil bacterial community structure and microbial biomass, which in turn may impact soil fertility and plant productivity within agricultural soils

Spitzer reveals what's behind Orion's Bar

We present Spitzer Space Telescope observations of 11 regions SE of the Bright Bar in the Orion Nebula, along a radial from the exciting star theta1OriC, extending from 2.6 to 12.1'. Our Cycle 5 programme obtained deep spectra with matching IRS short-high (SH) and long-high (LH) aperture grid patterns. Most previous IR missions observed only the inner few arcmin. Orion is the benchmark for studies of the ISM particularly for elemental abundances. Spitzer observations provide a unique perspective on the Ne and S abundances by virtue of observing the dominant ionization states of Ne (Ne+, Ne++) and S (S++, S3+) in Orion and H II regions in general. The Ne/H abundance ratio is especially well determined, with a value of (1.01+/-0.08)E-4. We obtained corresponding new ground-based spectra at CTIO. These optical data are used to estimate the electron temperature, electron density, optical extinction, and the S+/S++ ratio at each of our Spitzer positions. That permits an adjustment for the total gas-phase S abundance because no S+ line is observed by Spitzer. The gas-phase S/H abundance ratio is (7.68+/-0.30)E-6. The Ne/S abundance ratio may be determined even when the weaker hydrogen line, H(7-6) here, is not measured. The mean value, adjusted for the optical S+/S++ ratio, is Ne/S = 13.0+/-0.6. We derive the electron density versus distance from theta1OriC for [S III] and [S II]. Both distributions are for the most part decreasing with increasing distance. A dramatic find is the presence of high-ionization Ne++ all the way to the outer optical boundary ~12' from theta1OriC. This IR result is robust, whereas the optical evidence from observations of high-ionization species (e.g. O++) at the outer optical boundary suffers uncertainty because of scattering of emission from the much brighter inner Huygens Region.Comment: 60 pages, 16 figures, 10 tables. MNRAS accepte

Influence of single nucleotide polymorphisms in COMT, MAO-A and BDNF genes on dyskinesias and levodopa use in Parkinson’s disease

Background: Clinical heterogeneity in the development of levodopa-induced dyskinesias suggests endogenous factors play a significant role in determining their overall prevalence. We hypothesised that single nucleotide polymorphisms (SNPs) in specific genes may result in a clinical phenotype conducive to an increased risk of dyskinesia. Methods: We examined the influence of SNPs in the catechol O-methyltransferase (COMT), monoamine oxidase A (MAO-A) and brain-derived neurotrophic factor (BDNF) genes on time to onset and prevalence of dyskinesias in a cohort of 285 pathologically confirmed Parkinson’s disease patients. Results: Dyskinetic patients demonstrated younger age at disease onset (60.3 years vs. 66.4 years, p<0.0001), a longer disease duration (17.0 years vs. 12.0 years, p<0.0001) and a higher maximum daily levodopa equivalent dose (LED; 926.7 mg/day vs. 617.1 mg/day, p<0.0001) than patients without dyskinesias. No individual SNP was found to influence prevalence or time to onset of dyskinesias, including after adjustment for age at disease onset, disease duration, and maximum daily LED. We observed that patients carrying alleles conferring both high COMT activity and increased MAO-A mRNA expression received significantly higher maximum and mean daily LEDs than those with low enzyme activity/mRNA expression (max LED: 835mg ± 445mg vs. 508mg ± 316mg; p=0.0056, mean LED: 601mg ± 335mg vs. 398mg ± 260mg; p=0.025). Conclusions: Individual SNPs in BDNF, COMT and MAO-A genes did not influence prevalence or time to onset of dyskinesias in this cohort. The possibility that combined COMT and MAO-A genotype is a significant factor in determining an individual’s lifetime levodopa exposure warrants further investigation

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (λ) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty (“Forward” scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores (“Viterbi” scores) are Gumbel-distributed with constant λ = log 2, and the high scoring tail of Forward scores is exponential with the same constant λ. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments