Paving the crossroad of biorefinery

This thesis focuses on anaerobic digestion and, more specifically, on its role in biorefinery and on the dynamic behaviour of the underlying microbiomes. In recent decades, significant progress has been made in the field of anaerobic digestion. Innovative methods, especially highthroughput sequencing approaches, have allowed for a deeper understanding of biotechnologically relevant biocenosis. However, the exact behaviour of the relevant microbiomes under different conditions has not been thoroughly researched. In order to shed light on the diversity of the underlying biocenosis, this thesis compares multiple biogas production facilities in Germany. It also provides the first multi-OMICs characterization of separated acidification stages at mesophilic and thermophilic conditions. At the phylum level, three key microbiomes are identified, which are specific for sewage sludge, highly viscous codigester sludge, and leachate from leach-bed systems. All three microbiomes are strongly related to their underlying environmental parameters (Chemical oxygen demand, total organic carbon, total nitrogen contents, conductivity, total volatile fatty acids, total solids, volatile solids, pH, and volume of biogas). Through various experiments, new methods for acidifying biomass in pretreatment stages were investigated. One of the main contributions of this thesis is to highlight the importance of separated acidification stages as crossroad for multiple industries. Separated acidification potentially allows for the production of multiple organic acids, the usage of many varieties of waste, and the production of hydrogen simultaneously. Moreover, separated acidification might facilitate the usage of substrates that are difficult to digest, such as lignocellulose grass biomass or nitrogen-rich chicken dung. Indeed, this thesis demonstrates that both substrates can contribute to successful liquefaction. In searching for further possible applications based on acidification stages, we developed the first Microbial Thermoelectric Cell (MTC), which is compatible with anaerobic digestion and suitable for use in the pre-treatment stage. The MTC allows for the simultaneous production of ethanol and electric energy. Remnants might be used in a subsequent methane-producing stage. In addition, in seeking further new pretreatment methods, we investigated the possibility of combining thermal pre-treatment with microbe-driven acidification. Surprisingly, we observed only minimal impacts of heat-shocks in the microbial composition. Therefore, it might be possible in the future to combine heatshocks with acidification processes to improve biomass pre-treatment. Furthermore, this possibility highlights the robustness of microbiomes from anaerobic digestion processes. Finally, we isolated news strains from the acidification of grass biomass, with foreseeable roles in anaerobic digestion.This thesis focuses on anaerobic digestion and, more specifically, on its role in biorefinery and on the dynamic behaviour of the underlying microbiomes. In recent decades, significant progress has been made in the field of anaerobic digestion. Innovative methods, especially highthroughput sequencing approaches, have allowed for a deeper understanding of biotechnologically relevant biocenosis. However, the exact behaviour of the relevant microbiomes under different conditions has not been thoroughly researched. In order to shed light on the diversity of the underlying biocenosis, this thesis compares multiple biogas production facilities in Germany. It also provides the first multi-OMICs characterization of separated acidification stages at mesophilic and thermophilic conditions. At the phylum level, three key microbiomes are identified, which are specific for sewage sludge, highly viscous codigester sludge, and leachate from leach-bed systems. All three microbiomes are strongly related to their underlying environmental parameters (Chemical oxygen demand, total organic carbon, total nitrogen contents, conductivity, total volatile fatty acids, total solids, volatile solids, pH, and volume of biogas). Through various experiments, new methods for acidifying biomass in pretreatment stages were investigated. One of the main contributions of this thesis is to highlight the importance of separated acidification stages as crossroad for multiple industries. Separated acidification potentially allows for the production of multiple organic acids, the usage of many varieties of waste, and the production of hydrogen simultaneously. Moreover, separated acidification might facilitate the usage of substrates that are difficult to digest, such as lignocellulose grass biomass or nitrogen-rich chicken dung. Indeed, this thesis demonstrates that both substrates can contribute to successful liquefaction. In searching for further possible applications based on acidification stages, we developed the first Microbial Thermoelectric Cell (MTC), which is compatible with anaerobic digestion and suitable for use in the pre-treatment stage. The MTC allows for the simultaneous production of ethanol and electric energy. Remnants might be used in a subsequent methane-producing stage. In addition, in seeking further new pretreatment methods, we investigated the possibility of combining thermal pre-treatment with microbe-driven acidification. Surprisingly, we observed only minimal impacts of heat-shocks in the microbial composition. Therefore, it might be possible in the future to combine heatshocks with acidification processes to improve biomass pre-treatment. Furthermore, this possibility highlights the robustness of microbiomes from anaerobic digestion processes. Finally, we isolated news strains from the acidification of grass biomass, with foreseeable roles in anaerobic digestion

Bisphenol A: Quantification in Complex Matrices and Removal by Anaerobic Sludges

The endocrine disruptor bisphenol A (BPA) is one of the most commonly found micropollutants in the environment. However, the biodegradation of BPA under anaerobic (methanogenic) conditions is still an understudied process in wastewater treatment systems. The current study thus addresses the need for a simple and user-friendly analytical method for the rapid and accurate quantification of BPA in complex matrices such as digested and co-digester sludges. We established a microwave-assisted extraction method, followed by derivatization and gas chromatography–mass spectrometry to quantify BPA by comparing it with a deuterated internal standard. The BPA removal capabilities of three digester sludges and three co-digester sludges were examined under mesophilic methanogenic conditions in biogas plants. The endogenous BPA concentration (dry weight) ranged from 1596 to 10,973 µg kg −1 in digested sewage sludges, and from below the limit of quantification to 9069 µg kg −1 in co-digester sludges. When BPA was added to the sludges, the removal capabilities ranged from not significant to 50% after 21 days of incubation. Biogas production was unaffected by the addition of BPA (228 µg kg −1 ) to the aqueous sludge. The study demonstrated that BPA could be removed under anaerobic conditions in accustomed inoculates. The findings have far-reaching implications for understanding BPA persistence and detoxification under anaerobic conditions

Towards a Microbial Thermoelectric Cell

Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250–600 mV was achieved with 1.7 L baker’s yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices

Towards Quantum Sensing of Chiral-Induced Spin Selectivity: Probing Donor-Bridge-Acceptor Molecules with NV Centers in Diamond

Photoexcitable donor-bridge-acceptor (D-B-A) molecules that support intramolecular charge transfer are ideal platforms to probe the influence of chiral-induced spin selectivity (CISS) in electron transfer and resulting radical pairs. In particular, the extent to which CISS influences spin polarization or spin coherence in the initial state of spin-correlated radical pairs following charge transfer through a chiral bridge remains an open question. Here, we introduce a quantum sensing scheme to measure directly the hypothesized spin polarization in radical pairs using shallow nitrogen-vacancy (NV) centers in diamond at the single- to few-molecule level. Importantly, we highlight the perturbative nature of the electron spin-spin dipolar coupling within the radical pair, and demonstrate how Lee-Goldburg decoupling can preserve spin polarization in D-B-A molecules for enantioselective detection by a single NV center. The proposed measurements will provide fresh insight into spin selectivity in electron transfer reactions.Comment: 7 pages and 4 pages appendix including an extensive description of the initial spin state of photo-generated radical pair

Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis

A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism. © 2017 Abendroth et al

Spatially resolved surface dissipation over metal and dielectric substrates

We report spatially resolved measurements of static and fluctuating electric fields over conductive (Au) and non-conductive (SiO2) surfaces. Using an ultrasensitive `nanoladder' cantilever probe to scan over these surfaces at distances of a few tens of nanometers, we record changes in the probe resonance frequency and damping that we associate with static and fluctuating fields, respectively. We find that the two quantities are spatially correlated and of similar magnitude for the two materials. We quantitatively describe the observed effects on the basis of trapped surface charges and dielectric fluctuations in an adsorbate layer. Our results provide direct, spatial evidence for surface dissipation in adsorbates that affects nanomechanical sensors, trapped ions, superconducting resonators, and color centers in diamond

Single Nitrogen-Vacancy-NMR of Amine-Functionalized Diamond Surfaces

Nuclear magnetic resonance (NMR) imaging with shallow nitrogen-vacancy (NV) centers in diamond offers an exciting route toward sensitive and localized chemical characterization at the nanoscale. Remarkable progress has been made to combat the degradation in coherence time and stability suffered by near-surface NV centers using suitable chemical surface termination. However, approaches that also enable robust control over adsorbed molecule density, orientation, and binding configuration are needed. We demonstrate a diamond surface preparation for mixed nitrogen- and oxygen-termination that simultaneously improves NV center coherence times for emitters <10-nm-deep and enables direct and recyclable chemical functionalization via amine-reactive crosslinking. Using this approach, we probe single NV centers embedded in nanopillar waveguides to perform $^{19}\mathrm{F}$ NMR sensing of covalently bound trifluoromethyl tags in the ca. 50-100 molecule regime. This work signifies an important step toward nuclear spin localization and structure interrogation at the single-molecule level.Comment: 21 pages and 16 pages supporting informatio

Draft Genome Sequence of a New Oscillospiraceae Bacterium Isolated from Anaerobic Digestion of Biomass

Here, we present the genome sequence and annotation of the novel bacterial strain HV4-5-C5C, which may represent a new genus within the family Oscillospiraceae (order Eubacteriales). This strain is a potential keystone species in the hydrolysis of complex polymers during anaerobic digestion of biomass. © 2020 Pascual et al

Complete genome sequence of a new clostridium sp. isolated from anaerobic digestion and biomethanation

Here, we present the genome sequence and annotation of the bacterial strain HV4-5-A1G, a potentially new Clostridium species. Based on its genomic data, this strain may act as a keystone microorganism in the hydrolysis of complex polymers, as well as in the different acidogenesis and acetogenesis steps during anaerobic digestion. © 2020 Hahnke et al

Diamond surface engineering for molecular sensing with nitrogen-vacancy centers

Quantum sensing using optically addressable atomic-scale defects, such as the nitrogen--vacancy (NV) center in diamond, provides new opportunities for sensitive and highly localized characterization of chemical functionality. Notably, near-surface defects facilitate detection of the minute magnetic fields generated by nuclear or electron spins outside of the diamond crystal, such as those in chemisorbed and physisorbed molecules. However, the promise of NV centers is hindered by a severe degradation of critical sensor properties, namely charge stability and spin coherence, near surfaces (< ca. 10 nm deep). Moreover, applications in the chemical sciences require methods for covalent bonding of target molecules to diamond with robust control over density, orientation, and binding configuration. This forward-looking Review provides a survey of the rapidly converging fields of diamond surface science and NV-center physics, highlighting their combined potential for quantum sensing of molecules. We outline the diamond surface properties that are advantageous for NV-sensing applications, and discuss strategies to mitigate deleterious effects while simultaneously providing avenues for chemical attachment. Finally, we present an outlook on emerging applications in which the unprecedented sensitivity and spatial resolution of NV-based sensing could provide unique insight into chemically functionalized surfaces at the single-molecule level.Comment: Review paper, 36 page