The effect of acidogenic and methanogenic conditions on the availability and stability of carbon, nitrogen and phosphorus in a digestate

Acidification and drying of digestate are important post-treatment for, respectively, improving nutrient availability and hygiene. These approaches are expected to reduce digestate soil application mass and increase its value. This study compared eleven organic feedstocks under acidogenic and methanogenic conditions as a sustainable approach to improving phosphorus availablity, organic carbon and stabilising ammoniacal nitrogen of the resulting digestate under thermal drying. The result showed increases in phosphate concentration under acidogenic conditions and reduction in ammonium nitrogen after drying at 100 °C. The highest phosphate values of 3.2 ± 0.38 g/kg were achieved using whey permeate substrate while the effect of drying on ammonium nitrogen concentration was lowest for acidogenic bird seed fermentation with an ammonium loss of 59.7%. Both results were facilitated by high total volatile fatty acid concentration produced from available organic carbon which reached a maximum value of 5.71 ± 0.53 g/L, respectively. Increases in phosphate and ammonium nitrogen stability under acidogenic conditions was a consequence of lower pH, a condition synonymous with acidogenic only fermentation. The accumulated volatile fatty acid contributed to higher carbon to nitrogen ratio under acidogenic fermentation. Higher labile carbon to nitrogen ratio can trigger immobilization of ammonium nitrogen in the soil and this presents a case for subsequent experimentation into acidogenic digestate application in soil

Impact of organic amendments on the development of 14C-phenanthrene catabolism in soil

This study investigated the impact of spent brewery grains and spent mushroom compost on the development of phenanthrene biodegradation in soil. Two aspects were considered: (i) the influence of increasing waste-to-soil ratios (1:10, 1:5, 1:2, 1:1 & 2:1) and (ii) the impact of soil-PAH contact time (1–100 d). Biodegradation was quantified by measuring changes in the lag phase, the fastest rates and extents of mineralization of 14C-phenanthrene, as well as changes in the number of total heterotrophic and phenanthrene degrading bacteria and fungi. The amendment of smaller amounts of the wastes (1:10 & 1:5) resulted in greatest levels of biodegradation. Microbial numbers increased in all of the amended soils but phenanthrene-degrading numbers in most amended soils did not correlate with the rates and extents of 14C-phenanthrene mineralization. This investigation highlighted the value of waste organic materials as nutrient sources to stimulate microbial degradation of contaminants in soil

Soil contamination in China:Current priorities, defining background levels and standards for heavy metals

The Chinese Government is working to establish an effective framework in managing soil contamination. Heavy metal contamination is key to the discussion about soil quality, health and remediation in China. Soil heavy metal contamination in China is briefly reviewed and the concepts of background values and standards discussed. The importance of contaminated land and its management for China food security and urbanization are discussed. Priorities for China's next steps in developing an effective research and management regime are presented. We propose that critically important to the science-based risk assessment of contaminants in soils is the incorporation of speciation and bioavailability into the measurement and evaluation criteria. Consideration of soil biology/ecological endpoints will be necessary to protect ecosystem health. National and regional/local scenarios of land use type/usage will address residential/urban re-use of industrial land as well as varying agricultural scenarios

Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.Comment: 15 page

The effect of organic acids on the behaviour and biodegradation of 14C-phenanthrene in contaminated soil

The interaction between root exudates and soil microbes has been hypothesised as the primary mechanism for the biodegradation of organic pollutants in the rhizosphere. However, the mechanisms governing this loss process are not completely understood. This study aimed to investigate the effect of two important compounds within root exudates (citric and malic acid) on 14C-phenanthrene desorption and bioaccessibility in soil. Overall results showed that the presence of both citric and malic acid (>100 mmol l−1) enhanced the desorption of 14C-phenanthrene; this appeared to be concentration dependant. Increases in extractability were not reflected in a higher bioaccessibility. Despite enhancing the desorption of 14C-phenanthrene in soil, there is no direct evidence indicating that citric or malic acid have the ability to promote the biodegradation of 14C-phenanthrene from soil. Results from this study provide a novel understanding of the role that substrates, typically found within the rhizosphere due to root exudation, play in the bioaccessibility and biodegradation of hydrocarbons in contaminated soil

From bioavailability science to regulation of organic chemicals

The bioavailability of organic chemicals in soil and sediment is an important area of scientific investigation for environmental scientists, although this area of study remains only partially recognized by regulators and industries working in the environmental sector. Regulators have recently started to consider bioavailability within retrospective risk assessment frameworks for organic chemicals; by doing so, realistic decision-making with regard to polluted environments can be achieved, rather than relying on the traditional approach of using total-extractable concentrations. However, implementation remains difficult because scientific developments on bioavailability are not always translated into ready-to-use approaches for regulators. Similarly, bioavailability remains largely unexplored within prospective regulatory frameworks that address the approval and regulation of organic chemicals. This article discusses bioavailability concepts and methods, as well as possible pathways for the implementation of bioavailability into risk assessment and regulation; in addition, this article offers a simple, pragmatic and justifiable approach for use within retrospective and prospective risk assessmen

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Occurrence and Distribution of Polycyclic Aromatic Hydrocarbons and Nitrogen-Containing Polycyclic Aromatic Hydrocarbon Analogues in Soils from the Niger Delta, Nigeria

Polycyclic aromatic hydrocarbons (PAHs) and the nitrogen heterocyclic analogues (N-PAHs) are known to co-exist in environmental samples. Despite the known toxicity in polluted soils, their distribution remains to be elucidated in specific regions. This study investigated the occurrence and distribution PAHs and N-PAHs in soils from the Niger Delta. Physico-chemical analysis shows that Niger Delta soils are calcic, low in cation-exchange capacity (CEC); with ƩPAHs and ƩN-PAHs ranges of 663.9–1,618,821.2 µg/kg and 488.2–3,510.3 µg/kg, respectively. The most abundant PAHs were 2,6-dimethyl-naphthalene and 4,7-phenanthroline. Petrogenic-PAHs dominated the crude oil spill sites; while, pyrogenic-PAHs were abundant in drilling and gas flaring sites. Oil spill sites recorded elevated levels of N-PAHs, with 3-rings and carcinogenic-N-PAHs showing dominance. Furthermore, ƩPAHs and ƩN-PAHs in the oil rich region exceeded the Alberta and Canadian soil quality guidelines and, are also higher than PAHs/N-PAHs studies in literature. Risk assessment based on Benzo[a]pyrene toxic equivalency (TEQ-B[a]Peq) suggests high ecological risks. This is the first study on the occurrence and distribution of PAHs/N-PAHs in the area, and the data could serve a baseline purpose for risk assessment and remediation of contaminated sites

Respiration Responses of Earthworm to Soil Amended with Phenanthrene and the Nitrogen Heterocyclic Analogues

A disturbance in the normal physiology of soil macroinvertebrates can cause toxic impacts and/or disruption in mechanisms and rates of respiration. In this work, respiration rates of earthworms exposed to phenanthrene and its nitrogen heterocyclic analogs was investigated over a 30 and 90-d soil-contact-time. The study involved measurement and calculation of CO2 production by earthworms exposed to phenanthrene–N-PAHs amended soils. Data showed that N-PAH chemicals mostly affected the respiration rates of the earthworms compared to the homologous-PAH analog over time. The concentration–time plots showed greater respiration with increase in concentration over time. Calculated respiration inhibition-effect (%) revealed that phenanthrene had low degree of inhibition (27%) in the first 30-d at the highest concentration, while, NPAHs exhibited high degree of inhibitions (>45%) on respiration/physiological function of the exposed earthworms over the 90-d contact-time. Among the N-PAH chemicals, benzo[h]quinoline recorded >25% inhibition even at the lowest concentration (30-d). Statistical analysis of data revealed that N-PAHs maintained strong positive correlation on respiration response of the organisms with increased concentration and time (R2 = 0.803–0.997, p < .05). This suggests that N-PAH chemicals may have caused severe metabolic and physiological stress/inhibitions to soil organisms. Furthermore, the use of earthworm’s respiration rate in polluted soils could likely reshape the understanding of environmental stressors and serve as an early warning indicator for potential ecosystem shifts