Tracking N-cycling genes in biochar-supplemented ecosystems: A perspective

Introduction Since biochar has the potential to mitigate climate change and enhance agricultural outputs, new research is exploring its dual role relative to greenhouse gas emissions from agronomic soils, with particular focus on nitrous oxide (N2O). It is well accepted that definitive investigations of sustainable contemporary biochar applications in different (bio)technologies must be underpinned by combined physico-chemical and microecophysiological analyses. Nevertheless, recent nitrogen cycle research has measured principally the occurrence and emission of different N species to then infer shifts in microbial activity in response to biochar augmentation, with a few emerging studies assessing its effects on the functional genes/communities. As a result, a wide scope for critical and exciting research exists. This must be informed by comprehensive multidisciplinary studies of the dynamics of functional N-cycle genes, enzymes, strains and communities across different ecosystems and environmental biotechnologies – agriculture, contaminant remediation, wastewater treatment, malodorant gas biofiltration and landfill. This review aims to summarize the state-of-the art and highlight critical research that is required to assess the effect of biochar addition on N-cycling in different ecosystems. Conclusion We conclude that despite emerging research there are still critical knowledge gaps on the microbial response to biochar, which need to be addressed before the material can be applied in specific key environmental biotechnologies

A comparative in situ decomposition study using still born piglets and leaf litter from a deciduous forest

A cadaver and dead plant organic matter, or litter, are rich energy sources that undergo a complex decomposition process, which impact the surrounding environmental microbiota. Advances in molecular microbiology techniques, with study of the 16S RNA genes, in particular, have highlighted the application of forensic ecogenomics in addressing key knowledge gaps. To investigate subsurface microbiome shifts as a novel tool to establish “postmortem microbial clock” and augment postmortem interval (PMI) and time-since-burial estimations, an in situ study with triplicate underground burials of piglets as human taphonomic proxies and Quercus robur leaf litter was monitored for 270 days. Changes in microbial community structure and composition were related directly to changes in seasonal temperature, with microbial shifts more pronounced during the summer. For example, Methylococcaceae could be used as seasonal bacterial indicators, from winter to summer, in establishing postmortem microbial clock for this site. Furthermore, Methylophilaceae (Methylophilales order) and Anaerolineaceae would differentiate for the piglet and leaf litter soils, respectively, 180 days after internment

Ecological Media Reveal Community Structure Shifts in a Municipal Wastewater Treatment Train

Unique ecological/habitat media derived from four phases of a municipal wastewater treatment plant revealed the highest diversity (2.55-2.86) and evenness (0.79-0.87) for the raw sewage (R) medium. Richness was, however, inoculum- and media-dependent hence inocula R and P recorded the highest counts on media A and F, respectively

Anaerobic digestion in a multi-stage plug flow bioreactor: Revisiting an age-old process with modern molecular tools

To address knowledge gaps in the complex interacting microbial associations that underpin anaerobic digestion, a mesophilic (25°C) continuous-flow four-stage reactor was constructed to separate both spatially and temporally the component microbial groups. The reactor influent consisted of primary settled sewage sludge (PSSS) and the organic fraction of municipal solid waste (OFMSW). Chemical (volatile fatty acids, sulphate, sulphide, chemical oxygen demand, gas) and molecular analyses were made during an operation period of 15 months. Spatial separation of the microbial groups resulted in process instability where acidogenesis/acetogenesis produced an effluent with a pH between 2 and 4 that inhibited the subsequent catabolic steps. An organic loading rate of 6.5 g COD d-1 prevented reactor acidification but resulted in low biogas production (0.04-0.12 l biogas l-1 hydraulic load d-1). Fluctuations in chemical and molecular profiles/characteristics, which may have been due to the inherently heterogeneous PSSS and OFMSW, were recorded and these were countered by the development of a model medium. The medium was then used to: explore reactor efficacy; and study pertinent microbial diversity and functional interactions

Engaging students in bioscience research to improve their learning experience

Combining teaching and research is the definitive principle of ‘research-informed teaching’ (RIT) (Healey, 2005). RIT is pivotal for improving the student learning experience. All undergraduate students within the School of Science and Engineering, Teesside University (TU), can become RIT co-creators via their curricula-based Level 5 project proposal module and Level 6 research project. This case study illustrates how the authors used complementary, co-curricula methods to enhance student engagement with bioscience research utilising co-designed research projects and publication preparation. The success of student involvement in these initiatives was measured against six key personal attributes (Adaptable, Articulate, Aspiring, Creative, Critical, Confident), questionnaire responses from ten respondents, and a summary of tangible research outputs. An evaluation of staff involvement was made with semi-structured interviews. Overall, the research-led, partnership approach resulted in increased student motivation, aspiration and confidence in their further learning and employment

Soil metabarcoding identifies season indicators and differentiators of pig and Agrostis/Festuca spp decomposition

To gain a better understanding of how environmental microbiota respond to cadaver decomposition, a forensic ecogenomic study was made with soil only control and 4 g each of S. scrofa domesticus and plant litter (Agrostis/Festuca spp) buried individually in a sandy clay loam (80 g) in sealed but perforated triplicate microcosms. The next-generation sequencing (Illumina Miseq) of the soil bacteria (16S rRNA gene) clade revealed seasonal taxomonic shifts at genus-level for the pig and plant litter microcosms compared to the non-burial controls. In particular, numerical abundances of Sphingobacterium (5.9%) and Pedobacter (24.1%) for the pig microcosms, and Rhodanobacter (18.1%) and Shinella (4.6%) for the plant litter microcosms, identified bacterial genera that could be tracked to establish a (seasonal) subsurface postmortem microbial clock. Also, family-level resolution revealed members that were unique to the control, grass and pig soils after 365 days

Characterisation of indigenous microbial community isolated from wastewater treatment phases Baghdad/Iraq

Biodegradation processes could be efficient for such organic contaminants like o-xylene within sewage. Since the biodegradation processes is mainly controlled by microbial communities therefore, this research paper intended that the bioaugmentation process application might speed up or improve biodegradation process in Rustumihia plant. It delivers an initial knowledge of the effects of one of the most complicated organic contaminants at Rustumihia plant. In addition to that, it suggested the using of indigenous microbial communities that is isolated from the treatment plant within the application of bioaugmentation. It reveals findings on the ecology of o-xylene degradation via using bacterial communities that were already enriched and isolated from the four important treatment phases of Iraq's Rustumihia plant

Editorial: Life and Death: New Perspectives and Applications in Forensic Science

Death is a universal phenomenon and what happens after life has led to extensive forensic ecology research. Consequently, we now know that the shell of the once living provides fertile ground for other life forms, spanning prokaryotic microbes to large, vertebrate scavengers. This ephemeral patch of newly available resources also provides rich sources of evidence that can be used in death investigation. In recent years there have been substantial advances in technology that have facilitated the research and application of human remains decomposition in ways that harness theory and basic understanding of the ecological and evolutionary sciences (Tomberlin et al., 2011). To that end, this special issue covers the most recent perspectives and research that explores the complex ways that the once living can provide important information to the forensic sciences, in ways that can ultimately be applied to the judicial system and its processes. It is within this context of linking basic research in death and decomposition to applications of forensics that the special topic was born

Evaluating attenuated total reflectance infrared and near infrared spectroscopy for classifying M. musculus grave soil in the presence of clothing material

Objectives: Common methods utilised for establishing the time elapsed for unattended death scenes rely on physical atrophy. Predicting postmortem interval (PMI) relies on visual inspection, total body scoring and rigor mortis where the three are influenced by biotic and/or abiotic variables. These variables include the presence of different types of textiles that affect the cadaver decomposition island (CDI) in the type of fluids and decomposition products in the surrounding environment. Therefore, this work explores the impact of clothing material on the formation and timeline of CDI in simulated grave soil using attenuated total reflectance Fourier transform infrared (ATR-FTIR) and near infrared (NIR) spectroscopy. Materials and Methods: Grave soil evaluated in this study included samples that had carrions under different conditions including: (1) unwrapped carrions, (2) wrapped carrions with three types of fabric being cotton, polyester and viscose. Samples were stored in boxes and monitored over 170 days for environmental factors (temperature, pH, humidity) and for physicochemical properties. Physicochemical properties were determined using ATR-FTIR and NIR spectroscopy. Wrapped and unwrapped soil samples were measured frequently at weekly intervals through glass vials for NIR spectra or by placing 1-2 mg of soil on the diamond accessory for ATR-FTIR spectra. In both cases, spectra were exported into Matlab 2019a where spectral interpretation and analysis were applied. Spectral interpretation comprised comparing the absorbances obtained for soil samples against the reported literature. Spectral analysis involved applying principal component analysis (PCA) that informed about patterns in the absorbances of soils both unwrapped and wrapped with different fabrics. Results: Both ATR-FTIR and NIR spectra informed about the chemical and physical profile of soil samples with unwrapped and wrapped cadavers. ATR-FTIR spectra highlighted shifts in both O-H stretching and bending bands at ~3300 cm-1 and ~1640 cm-1, respectively. Grave soil associated with M. musculus exhibited increased intensity at ~1250 cm-1 C-O-C ester stretching, indicative of volatile organic compounds that produce the characteristic smell of death. This peak was delayed significantly in response to wrapping in various textiles. Although bands relating to lipid (~1760 cm-1) and protein (1690/1680 cm-1) degradation were identified on ATR spectra from the textiles post-exhumation, these were not identified in the respective soil samples. Both symmetrical and asymmetrical CH2 wagging present at 2920 cm-1 and 2850 cm-1, suggested the presence of saturated and unsaturated fatty acids. NIR spectra also highlighted temporal changes in -OH bonds (1420 nm). Although not highlighted by ATR, amides and amine secondary and tertiary overtone profiles, were detectable in soil samples associated with decomposing M. musculus between 1000 and 1200 nm. When PCA was applied to both types of spectra, it showed its ability to distinguish between the different types of fabric that the cadavers had been wrapped with. Conclusions: Our findings showed that ATR-FTIR and NIR spectroscopy offered a non-destructive approach to understand the decomposition of cadaver remains in soil. Moreover, both techniques informed about the impact about different textiles on the formation of CDI. In this respect, the presence of textiles has delayed CDI formation. By combining both techniques with PCA, soil samples could be classified indicating to the type of fabric the cadaver had been wrapped with

Evaluating Attenuated Total Reflectance Fourier Transform Infrared to Identify and Delineate Gravesoil Post-Exhumation of a Murine Carrion

Understanding remains removal and relocation provides intelligence aiding in the accuracy of post-mortem interval estimation (PMI), formulating a timeline of events in subsequent death inquests. The quantitative longevity of the chemical cadaver decomposition island (CDI) regarding translocation of remains is particularly pertinent at historical and cold-case crime scenes. This study aimed to track shifts in subsurface soil physicochemistry in simulation burial microcosms where adult Mus musculus were utilised as human cadaver proxies. Soil samples were taken from the microcosms over 170 days post-exhumation of 8, 16, 24 and 32 days of initial burial (n=3). Physicochemical properties of the gravesoil were obtained non-destructively using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. ATR-FTIR spectra highlighted temporal delineation of microcosms on the basis time-since-removal of remains. Changes in the both symmetrical and asymmetrical CH2 wagging present at -~2920 cm-1 and ~2850 cm-1 , indicative of aliphatic chain lipids, were prolonged significantly in post-exhumation soils when the carrion was removed after 3 and 4 weeks of burial