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

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

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

Microbial Ecogenomics and Forensic Archaeology: New Methods for Investigating Clandestine Gravesites

In the mid-1990s, the crime scene toolkit was revolutionised by the introduction of DNA-based analyses such as the polymerase chain reaction, low copy number DNA analysis, short-tandem repeat typing, pulse-field gel electrophoresis and variable number tandem repeat. Since then, methodological advances in other disciplines, especially molecular microbial ecology, can now be adapted for cutting-edge applications in forensic contexts. Despite several studies and discussions, there is, however, currently very little evidence of these techniques’ adoption at the contemporary crime scene. Consequently, this article discusses some of the popular ‘omics’ and their current and potential exploitations in the ‘forensic ecogenomics’ of body decomposition in a crime scene. Thus, together with published supportive findings and discourse, knowledge gaps are identified. These then justify the need for more comprehensive, directed, concerted and global research towards state-of-the-art microecophysiology method application and/or adaptation for subsequent successful exploitations in this additional context of microbial forensics

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 quality of the student learning experience. All undergraduate students within the School of Science and Engineering, Teesside University (TU), are given the opportunity to become RIT co-creators via curricula mechanisms, primarily via a second year project proposal module combined with their final year project. This case study aims to illustrate how, over three academic years, the authors used co-curricula methods to enhance student engagement within the bioscience research environment 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 and Aspiring, Creative, Critical, Confident) and questionnaire responses from a total of ten respondents, in addition to a summary of tangible research outputs. An evaluation of staff involvement was also considered through the use of semi-structured interviews. Also outlined are the ways in which RIT can be integrated by early career researchers without significant financial input.Overall, the research-led, partnership approach resulted in increased student motivation, aspiration and confidence in their further learning and employment

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

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