Effect of Oxygen Contamination on Propionate and Caproate Formation in Anaerobic Fermentation

Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H$_{2}$/CO$_{2}$. Two stirred tank reactors and two bubble column reactors were operated with H$_{2}$/CO$_{2}$ gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O$_{2}$ L$^{-1}$ d$^{-1}$, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH$_{4}$ was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O$_{2}$ concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O$_{2}$ below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8–1.8 mmol L$^{-1}$ d$^{-1}$ depending on the reactor (control reactors 0.1–0.8 mmol L$^{-1}$ d$^{-1}$). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H$_{2}$ availability was high. After air contamination stopped completely, production of n-caproate and CH$_{4}$ recovered, with n-caproate production rates of 1.4–1.8 mmol L$^{-1}$ d$^{-1}$ (control 0.7–2.1 mmol L$^{-1}$ d$^{-1}$). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions

In situ microfluidic cryofixation for cryo Focused Ion Beam milling and cryo electron tomography.

We present a microfluidic platform for studying structure-function relationships at the cellular level by connecting video rate live cell imaging with in situ microfluidic cryofixation and cryo-electron tomography of near natively preserved, unstained specimens. Correlative light and electron microscopy (CLEM) has been limited by the time required to transfer live cells from the light microscope to dedicated cryofixation instruments, such as a plunge freezer or high-pressure freezer. We recently demonstrated a microfluidic based approach that enables sample cryofixation directly in the light microscope with millisecond time resolution, a speed improvement of up to three orders of magnitude. Here we show that this cryofixation method can be combined with cryo-electron tomography (cryo-ET) by using Focused Ion Beam milling at cryogenic temperatures (cryo-FIB) to prepare frozen hydrated electron transparent sections. To make cryo-FIB sectioning of rapidly frozen microfluidic channels achievable, we developed a sacrificial layer technique to fabricate microfluidic devices with a PDMS bottom wall <5 µm thick. We demonstrate the complete workflow by rapidly cryo-freezing Caenorhabditis elegans roundworms L1 larvae during live imaging in the light microscope, followed by cryo-FIB milling and lift out to produce thin, electron transparent sections for cryo-ET imaging. Cryo-ET analysis of initial results show that the structural preservation of the cryofixed C. elegans was suitable for high resolution cryo-ET work. The combination of cryofixation during live imaging enabled by microfluidic cryofixation with the molecular resolution capabilities of cryo-ET offers an exciting avenue to further advance space-time correlative light and electron microscopy (st-CLEM) for investigation of biological processes at high resolution in four dimensions

Relative CC"-Numerical Ranges for Applications in Quantum Control and Quantum Information

Motivated by applications in quantum information and quantum control, a new type of $C$"-numerical range, the relative $C$"-numerical range denoted $W_K(C,A)$, is introduced. It arises upon replacing the unitary group U(N) in the definition of the classical $C$"-numerical range by any of its compact and connected subgroups $K \subset U(N)$. The geometric properties of the relative $C$"-numerical range are analysed in detail. Counterexamples prove its geometry is more intricate than in the classical case: e.g. $W_K(C,A)$ is neither star-shaped nor simply-connected. Yet, a well-known result on the rotational symmetry of the classical $C$"-numerical range extends to $W_K(C,A)$, as shown by a new approach based on Lie theory. Furthermore, we concentrate on the subgroup $SU_{\rm loc}(2^n) := SU(2)\otimes ... \otimes SU(2)$, i.e. the $n$-fold tensor product of SU(2), which is of particular interest in applications. In this case, sufficient conditions are derived for $W_{K}(C,A)$ being a circular disc centered at origin of the complex plane. Finally, the previous results are illustrated in detail for $SU(2) \otimes SU(2)$.Comment: accompanying paper to math-ph/070103

Comparative analysis of methanogenic communities in different laboratory-scale anaerobic digesters

© 2016 Ayrat M. Ziganshin et al.Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase -subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors

Effects of the reduction of the hydraulic retention time to 1.5 days at constant organic loading in CSTR, ASBR, and fixed-bed reactors - Performance and methanogenic community composition

The hydraulic retention time (HRT) is one of the key parameters in biogas processes and often it is postulated that a minimum HRT of 10-25 days is obligatory in continuous stirred tank reactors (CSTR) to prevent a washout of slow growing methanogens. In this study the effects of the reduction of the HRT from 6 to 1.5 days on performance and methanogenic community composition in different systems with and without immobilization operated with simulated thin stillage (STS) at mesophilic conditions and constant organic loading rates (OLR) of 10gL-1d-1 of volatile solids were investigated. With the reduction of the HRT process instability was first observed in the anaerobic sequencing batch reactor (ASBR) (at HRT of 3 days) followed by the CSTR (at HRT of 2 days). The fixed bed reactor (FBR) was stable until the end of the experiment, but the reduction of the HRT to 1.5 days caused a decrease of the specific biogas production to about 450Lkg-1 of VS compared to about 600Lkg-1 of VS at HRTs of 4-5 days. Methanoculleus and Methanosarcina were the dominant genera under stable process conditions in the CSTR and the ASBR and members of Methanosaeta and Methanospirillum were only present at HRT of 4 days and lower. In the effluent of the FBR Methanosarcina spp. were not detected and Methanosaeta spp. were more abundant then in the other reactors. © 2014 Elsevier Ltd

Reduction of the hydraulic retention time at constant high organic loading rate to reach the microbial limits of anaerobic digestion in various reactor systems

© 2016 Elsevier LtdThe effects of hydraulic retention time (HRT) reduction at constant high organic loading rate on the activity of hydrogen-producing bacteria and methanogens were investigated in reactors digesting thin stillage. Stable isotope fingerprinting was additionally applied to assess methanogenic pathways. Based on hydA gene transcripts, Clostridiales was the most active hydrogen-producing order in continuous stirred tank reactor (CSTR), fixed-bed reactor (FBR) and anaerobic sequencing batch reactor (ASBR), but shorter HRT stimulated the activity of Spirochaetales. Further decreasing HRT diminished Spirochaetales activity in systems with biomass retention. Based on mcrA gene transcripts, Methanoculleus and Methanosarcina were the predominantly active in CSTR and ASBR, whereas Methanosaeta and Methanospirillum activity was more significant in stably performing FBR. Isotope values indicated the predominance of aceticlastic pathway in FBR. Interestingly, an increased activity of Methanosaeta was observed during shortening HRT in CSTR and ASBR despite high organic acids concentrations, what was supported by stable isotope data

Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough

http://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt08-13/

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

All sequence data from this study were deposited at the European Bioinformatics Institute under the accession numbers ERS1670018 to ERS1670023. Further, all assigned genes, taxonomy, function, sequences of contigs, genes and proteins can be found in Table S3.In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (2136% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.This study was supported by a grant of BE-Basic-FES funds from the Dutch Ministry of Economic Affairs. The research of A.J.M. Stams is supported by an ERC grant (project 323009) and the gravitation grant “Microbes for Health and Environment” (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science. F. Hugenholtz was supported by the same gravitation grant (project 024.002.002). B. Hornung is supported by Wageningen University and the Wageningen Institute for Environment and Climate Research (WIMEK) through the IP/OP program Systems Biology (project KB-17-003.02-023).info:eu-repo/semantics/publishedVersio