Microbial community metabolic concurrence involved in toluene degradation: effect of oxygen availability on catabolic gene expression of aerobic and anaerobic toluene degrading bacteria

Bakterien sind in ihrer natürlichen Umgebung permanent mit variierenden Sauerstoffgradienten, wie sie z.B. in Grundwasserleitern, mikrobiellen Matten und im Wurzelraum von Pflanzen, der Rhizosphäre, existieren, konfrontiert. Schadstoffabbauende Mikroorganismen haben zudem die Fähigkeiten entwickelt, sich mit Hilfe adaptiver Mechanismen und der Regulation ihrer katabolen Gene an die sich permanent ändernden Umweltbedingungen kontaminierter Standorte anzupassen. In dieser Arbeit wurde die relative Expression kataboler Gene unter oszillierenden Sauerstoffkonzentrationen von zwei Schadstoff-abbauenden Bakterien, dem aeroben Toluol-Abbauer, Pseudomonas putida mt-2 (der das TOL Plasmid pWW0 enthält), und dem anaeroben Toluol-Abbauer, Thauera aromatica K172 untersucht. Die katabolen Gene waren dabei xylM und xylE für P. putida, sowie bssA und bcrA für T. aromatica

Taking the TU Delft Carpentries Workshops Online

Due to the COVID-19 pandemic, Delft University of Technology in the Netherlands (TU Delft) stopped its activities on campus until autumn 2021 and moved all teaching activities to an online setting. This article describes the challenges and lessons learned from successfully moving basic programming workshops, Software Carpentry workshops, online. The article details the local TU Delft context, the online workshop tools that were employed, and the roles that the organising team played to organise and run these online workshops. To successfully adapt to the online context, it was important to adjust the original planning and programme for the Carpentry workshops. General challenges of online workshops and solutions that worked for the TU Delft team are also shared. Through iteratively developing the online workshops over the past year, the team has enhanced both learners’ and organisers’ experience. The lessons learned will continue to be valuable when the workshops are transitioned back to a physical setting when COVID-19 protective measures are lifted

Isolation and characterization of <i>Magnetospirillum</i> sp strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model

Previously, Planted Fixed-Bed Reactors (PFRs) have been used to investigate microbial toluene removal in the rhizosphere of constructed wetlands. Aerobic toluene degradation was predominant in these model systems although bulk redox conditions were hypoxic to anoxic. However, culture-independent approaches indicated also that microbes capable of anaerobic toluene degradation were abundant. Therefore, we aimed at isolating anaerobic-toluene degraders from one of these PFRs. From the obtained colonies which consisted of spirilli-shaped bacteria, a strain designated 15-1 was selected for further investigations. Analysis of its 16S rRNA gene revealed greatest similarity (99%) with toluene-degrading Magnetospirillum sp. TS-6. Isolate 15-1 grew with up to 0.5 mM of toluene under nitrate-reducing conditions. Cells reacted to higher concentrations of toluene by an increase in the degree of saturation of their membrane fatty acids. Strain 15-1 contained key genes for the anaerobic degradation of toluene via benzylsuccinate and subsequently the benzoyl-CoA pathway, namely bssA, encoding for the alpha subunit of benzylsuccinate synthase, bcrC for subunit C of benzoyl-CoA reductase and bamA for 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Finally, most members of a clone library of bssA generated from the PFR had highest similarity to bssA from strain 15-1. Our study provides insights about the physiological capacities of a strain of Magnetospirillum isolated from a planted system where active rhizoremediation of toluene is taking place

Advancing Research Data Management in Universities of Science and Technology

The white paper ‘Advancing Research Data Management in Universities of Science and Technology’ shares insights on the state-of-the-art in research data management, and recommendations for advancement. A core part of the paper are the results of a survey, which was distributed to our member institutions in 2019 and addressed the following aspects of research data management (RDM): (i) the establishment of a RDM policy at the university; (ii) the provision of suitable RDM infrastructure and tools; and (iii) the establishment of RDM support services and trainings tailored to the requirements of science and technology disciplines. The paper reveals that while substantial progress has been made, there is still a long way to go when it comes to establishing “advanced-degree programmes at our major universities for the emerging field of data scientist”, as recommended in the seminal 2010 report ‘Riding the Wave’, and our white paper offers concrete recommendations and best practices for university leaders, researchers, operational staff, and policy makers. The topic of RDM has become a focal point in many scientific disciplines, in Europe and globally. The management and full utilisation of research data are now also at the top of the European agenda, as exemplified by Ursula von der Leyen addressat this year’s World Economic Forum.However, the implementation of RDM remains divergent across Europe. The white paper was written by a diverse team of RDM specialists, including data scientists and data stewards, with the work led by the RDM subgroup of our Task Force Open Science. The writing team included Angelina Kraft (Head of Lab Research Data Services at TIB, Leibniz University Hannover) who said: “The launch of RDM courses and teaching materials at universities of science and technology is a first important step to motivate people to manage their data. Furthermore, professors and PIs of all disciplines should actively support data management and motivate PhD students to publish their data in recognised digital repositories.” Another part of the writing team was Barbara Sanchez (Head of Centre for Research Data Management, TU Wien) and Malgorzata Goraczek (International Research Support / Data Management Support, TU Wien) who added:“A reliable research data infrastructure is a central component of any RDM service. In addition to the infrastructure, proper RDM is all about communication and cooperation. This includes bringing tools, infrastructures, staff and units together.” Alastair Dunning (Head of 4TU.ResearchData, Delft University of Technology), also one of the writers, added: “There is a popular misconception that better research data management only means faster and more efficient computers. In this white paper, we emphasise the role that training and a culture of good research data management must play.

<i>Delftia</i> sp LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation

BACKGROUND: Dimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems. RESULTS: In this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. The enzyme may also catalyze both monooxygenation reactions during the degradation of benzene. Proteome data led to the identification of catechol meta cleavage pathway enzymes during the growth on ortho DMP, and validated that cleavage of the aromatic rings of 2,5- and 3,5-DMPs does not result in mineralization. In addition, the tolerance of the strain to high concentrations of DMP, especially to 3,4-DMP was higher than that of other reported microorganisms from activated sludge treating phenols. CONCLUSIONS: LCW strain was able to degraded complex aromatics compounds. DMPs and benzene are reported for the first time to be degraded by a member of Delftia genus. In addition, LCW degraded DMPs with a first oxidation of the aromatic rings by a phenol hydroxylase, followed by a further meta cleavage pathway. The higher resistance to DMP toxicity, the ability to degrade and transform DMP isomers and the origin as a rhizosphere bacterium from wastewater systems, make LCW a suitable candidate to be used in bioremediation of complex DMP mixtures in CWs systems

Report on the Workshop on Sustainable Software Sustainability 2019 (WOSSS19)

This report is based on the discussions and presentations that took place at the Workshop on Sustainable Software Sustainability (www.software.ac.uk/wosss19) in April 2019 (WOSSS19). It captures the state of the art for a range of Software Sustainability themes that were brought up by the organisers and attendees of the workshop

Bringing Research Data Management to Academic Libraries

Modern research institutions are faced with rapidly increasing challenges imposed by data-driven science&nbsp;and have to deal with new demands from funding agencies and publishers regarding open access to&nbsp;research data as well as from the Code of Conduct for Research Integrity on reproducibility of results. In&nbsp;reply to these requirements, the Technical University of Denmark (DTU) has adapted a two-fold strategy of&nbsp;bringing together decision-makers, relevant support units in the administration and researchers from all&nbsp;departments for the task of designing policies and services in alignment with common traditions in the&nbsp;different fields of research. This mixed “bottom-up” / “top-down” approach ensures that best practices&nbsp; for&nbsp;research data management can be implemented in the daily routines of employees in a practical and&nbsp;supportive way while ensuring that the researchers can live up to all relevant administrative, legal and&nbsp;ethical standards.&nbsp; In this presentation, we will show how DTU Library has taken over a central position in this process by&nbsp;investigating the needs and demands from researchers in the different fields, drafting procedures and&nbsp;guidelines for research data management and establishing support functions and training for all aspects&nbsp; of&nbsp;the data life cycle. Within this new and complex area, the creation of new positions for research data&nbsp;management at the library in addition to an optimal utilization of existing resources and knowledge has&nbsp;been crucial for building up the necessary expertise and thus for the success of the strategy.&nbsp; AuthorsFalco Jonas Hüser, PhDProject Officer – Research Data Managementemail: [email protected] 0000-0001-9645-6691Paula Maria Martinez Lavanchy, PhDProject Officer – Research Data Managementemail: [email protected] 0000-0003-1448-091

DTU Research Data Life Cycle

Research Data Life Cycle used at the Technical University of Denmark, created by the DTU Office for Bibliometrics and Data Management