Towards smart biomanufacturing: a perspective on recent developments in industrial measurement and monitoring technologies for bio-based production processes.

The biomanufacturing industry has now the opportunity to upgrade its production processes to be in harmony with the latest industrial revolution. Technology creates capabilities that enable smart manufacturing while still complying with unfolding regulations. However, many biomanufacturing companies, especially in the biopharma sector, still have a long way to go to fully benefit from smart manufacturing as they first need to transition their current operations to an information-driven future. One of the most significant obstacles towards the implementation of smart biomanufacturing is the collection of large sets of relevant data. Therefore, in this work, we both summarize the advances that have been made to date with regards to the monitoring and control of bioprocesses, and highlight some of the key technologies that have the potential to contribute to gathering big data. Empowering the current biomanufacturing industry to transition to Industry 4.0 operations allows for improved productivity through information-driven automation, not only by developing infrastructure, but also by introducing more advanced monitoring and control strategies.

Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

Deep-sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high-temperature venting systems have been studied extensively, the microbiotas associated with low-temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian-Greenland Sea, applying an integrated 'omics' approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction-independent three-domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico-chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments.

Computational investigation of NOx emission in biogas combustion.

Landfills and anaerobic digesters in the waste treatment processes generate biogas. Biogas can be used as a fuel and excess biogas is typically burned in a flare to reduce the greenhouse effect. However, burning biogas produces several pollutants, including CO2, NOx, and SO2. To minimize these emissions, the amount of excess air used in the combustion process needs to be considered, which has a significant impact on NOx emissions. This study developed a Computational Fluid Dynamics (CFD) model to simulate a small-scale biogas combustion system and analyses the effect of excess air on heat output and NOx emissions during biogas combustion. The GRI-Mech reaction mechanism was used to simulate reactions, and the model was validated by comparing it to experimental data from the DLR-Stuttgart CH4/H2/N2 Jet Flame. To reduce computational costs, a Tabulation of Dynamic Adaptive Chemistry (TDAC) algorithm was used to dynamically adapt the reaction mechanism in real time. Turbulence in the DLR flame was simulated using Reynolds-Averaged Navier-Stokes (RANS). The CFD model used a co-flow of a natural draft to provide additional air, while the air was premixed with fuel. The CFD model was used to simulate various premixed equivalent ratios, and the resulting emissions and heat outputs were compared. The study found that the optimal premixed equivalent ratio for the studied system was between 0.85 and 1.1, as this range produced the highest temperature and lowest NOx emissions. This model facilitates emission analysis of gas-phase combustion systems.

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community.

Geodia barretti is a marine cold-water sponge harbouring high numbers of microorganisms. Significant rates of nitrification have been observed in this sponge, indicating a substantial contribution to nitrogen turnover in marine environments with high sponge cover. In order to get closer insights into the phylogeny and function of the active microbial community and the interaction with its host G. barretti, a metatranscriptomic approach was employed, using the simultaneous analysis of rRNA and mRNA. Of the 262 298 RNA-tags obtained by pyrosequencing, 92% were assigned to ribosomal RNA (ribo-tags). A total of 109 325 SSU rRNA ribo-tags revealed a detailed picture of the community, dominated by group SAR202 of Chloroflexi, candidate phylum Poribacteria and Acidobacteria, which was different in its composition from that obtained in clone libraries prepared form the same samples. Optimized assembly strategies allowed the reconstruction of full-length rRNA sequences from the short ribo-tags for more detailed phylogenetic studies of the dominant taxa. Cells of several phyla were visualized by FISH analyses for confirmation. Of the remaining 21 325 RNA-tags, 10 023 were assigned to mRNA-tags, based on similarities to genes in the databases. A wide range of putative functional gene transcripts from over 10 different phyla were identified among the bacterial mRNA-tags. The most abundant mRNAs were those encoding key metabolic enzymes of nitrification from ammonia-oxidizing archaea as well as candidate genes involved in related processes. Our analysis demonstrates the potential and limits of using a combined rRNA and mRNA approach to explore the microbial community profile, phylogenetic assignments and metabolic activities of a complex, but little explored microbial community.

Low temperature fabrication of spherical brushite granules by cement paste emulsion.

Secondary protonated calcium phosphates such as brushite (CaHPO(4)·2H(2)O) or monetite (CaHPO(4)) have a higher resorption potential in bone defects than sintered ceramics, e.g. tricalcium phosphate or hydroxyapatite. However, processing of these phosphates to monolithic blocks or granules is not possible by sintering due to thermal decomposition of protonated phosphates at higher temperatures. In this study a low temperature technique for the preparation of spherical brushite granules in a cement setting reaction is presented. These granules were synthesized by dispersing a calcium phosphate cement paste composed of ß-tricalcium phosphate and monocalcium phosphate together with a surfactant to an oil/water emulsion. The reaction products were characterized regarding their size distribution, morphology, and phase composition. Clinically relevant granule sizes ranging from 200 µm to 1 mm were obtained, whereas generally smaller granules were received with higher oil viscosity, increasing temperature or higher powder to liquid ratios of the cement paste. The hardened granules were microporous with a specific surface area of 0.7 m(2)/g and consisted of plate-like brushite (>95 % according to XRD) crystals of 0.5-7 µm size. Furthermore it was shown that the granules may be also used for drug delivery applications. This was demonstrated by adsorption of vancomycin from an aqueous solution, where a load of 1.45-1.88 mg drug per g granules and an almost complete release within 2 h was obtained.

Promoting the co-utilisation of glucose and xylose in lignocellulosic ethanol fermentations using a data-driven feed-back controller.

BACKGROUND: The diauxic growth of Saccharomyces cerevisiae on glucose and xylose during cellulose-to-ethanol processes extends the duration of the fermentation and reduces productivity. Despite the remarkable advances in strain engineering, the co-consumption of glucose and xylose is still limited due to catabolite repression. This work addresses this challenge by developing a closed-loop controller that is capable of maintaining the glucose concentration at a steady set-point during fed-batch fermentation. The suggested controller uses a data-driven model to measure the concentration of glucose from 'real-time' spectroscopic data. The concentration of glucose is then automatically controlled using a control scheme that consists of a proportional, integral, differential (PID) algorithm and a supervisory layer that manipulates the feed-rates to the reactor accounting for the changing dynamics of fermentation. RESULTS: The PID parameters and the supervisory layer were progressively improved throughout four fed-batch lignocellulosic-to-ethanol fermentations to attain a robust controller able of maintaining the glucose concentration at the pre-defined set-points. The results showed an increased co-consumption of glucose and xylose that resulted in volumetric productivities that are 20-33% higher than the reference batch processes. It was also observed that fermentations operated at a glucose concentration of 10 g/L were faster than those operated at 4 g/L, indicating that there is an optimal glucose concentration that maximises the overall productivity. CONCLUSIONS: Promoting the simultaneous consumption of glucose and xylose in S. cerevisiae is critical to increase the productivity of lignocellulosic ethanol processes, but also challenging due to the strong catabolite repression of glucose on the uptake of xylose. Operating the fermentation at low concentrations of glucose allows reducing the effects of the catabolite repression to promote the co-consumption of the two carbon sources. However, S. cerevisiae is very sensitive to changes in the glucose concentration and deviations from a set-point result in notable productivity losses. The controller structure developed and implemented in this work illustrates how combining data-driven measurements of the glucose concentration and a robust yet effective PID-based supervisory control allowed tight control of the concentration of glucose to adjust it to the metabolic requirements of the cell culture that can unlock tangible gains in productivities.

First detection of thiotrophic symbiont phylotypes in the pelagic marine environment.

Marine oligochaete and nematode thiotrophic symbionts (MONTS) form a phylogenetic cluster within the Gammaproteobacteria. For the symbionts that live on the nematode surface, environmental transmission is likely. However, until now, no free-living relatives have been found. In this study, we detected MONTS cluster members in offshore surface seawater of both the Caribbean and the Mediterranean Sea by PCR amplification of their 16S rRNA genes. This is the first evidence of members of this cluster in the pelagic environment. These may either be free-living forms of the symbionts or closely related, nonsymbiotic strains. In either case, their existence sheds light on the evolution of beneficial symbioses between shallow water invertebrates and sulfur-oxidizing bacteria.

Molecular characterization of the symbionts associated with marine nematodes of the genus Robbea.

Marine nematodes that carry sulfur-oxidizing bacteria on their cuticle (Stilbonematinae, Desmodoridae) migrate between oxidized and reduced sand layers thereby supplying their symbionts with oxygen and sulfide. These symbionts, in turn, constitute the worms' major food source. Due to the accessibility, abundance and relative simplicity of this association, stilbonematids may be useful to understand symbiosis establishment. Nevertheless, only the symbiont of Laxus oneistus has been found to constitute one single phylotype within the Gammaproteobacteria. Here, we characterized the symbionts of three yet undescribed nematodes that were morphologically identified as members of the genus Robbea. They were collected at the island of Corsica, the Cayman Islands and the Belize Barrier Reef. The surface of these worms is covered by a single layer of morphologically undistinguishable bacteria. 18S rDNA-based phylogenetic analysis showed that all three species belong to the Stilbonematinae, although they do not form a distinct cluster within that subfamily. 16S rDNA-based analysis of the symbionts placed them interspersed in the cluster comprising the sulfur-oxidizing symbionts of L. oneistus and of marine gutless oligochaetes. Finally, the presence and phylogeny of the aprA gene indicated that the symbionts of all three nematodes can use reduced sulfur compounds as an energy source.