Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community.

Recovery of high quality PCR-amplifiable DNA has been the general minimal requirement for DNA extraction methods for bulk molecular analysis. However, modern high through-put community profiling technologies are more sensitive to representativeness and reproducibility of DNA extraction method. Here, we assess the impact of three DNA extraction methods (with different levels of extraction harshness) for assessing hindgut microbiomes from pigs fed with different diets (with different physical properties). DNA extraction from each sample was performed in three technical replicates for each extraction method and sequenced by 16S rRNA amplicon sequencing. Host was the primary driver of molecular sequencing outcomes, particularly on samples analysed by wheat based diets, but higher variability, with one failed extraction occurred on samples from a barley fed pig. Based on these results, an effective method will enable reproducible and quality outcomes on a range of samples, whereas an ineffective method will fail to generate extract, but host (rather than extraction method) remains the primary factor.

The role of anaerobic digestion in the emerging energy economy.

Anaerobic digestion is the default process for biological conversion of residue organics to renewable energy and biofuel in the form of methane. However, its scope of application is expanding, due to availability of new technologies, and the emerging drivers of energy and nutrient conservation and recovery. Here, we outline two of these new application areas, namely wastewater nutrient and energy recovery, and generation of value added chemicals through mixed culture biotechnology. There exist two options for nutrient and energy recovery from domestic wastewater: low energy mainline and partition-release-recovery. Both are heavily dependent on anaerobic digestion as an energy generating and nutrient release step, and have been enabled by new technologies such as low emission anaerobic membrane processes. The area of mixed culture biotechnology has been previously identified as a key industrial opportunity, but is now moving closer to application due application of existing and new technologies. As well as acting as a core technology option in bioproduction, anaerobic digestion has a key role in residual waste valorization and generation of energy for downstream processing. These new application areas and technologies are emerging simultaneously with substantial advances in knowledge of underlying mechanisms such as electron transfer, understanding of which is critical to development of the new application areas.

Gas controlled hydrogen fermentation.

Acidogenic fermentation is an anaerobic process of double purpose, while treating organic residues it produces chemical compounds, such as hydrogen, ethanol and organic acids. Therefore, acidogenic fermentation arises as an attractive biotechnology process towards the biorefinery concept. Moreover, this process does not need sterile operating conditions and works under a wide range of pH. Changes of operating conditions produce metabolic shifts, inducing variability on acidogenic product yield. To induce those changes, experiments, based on reactor headspace N(2)-flushing (gas phase), were designed. A major result was the hydrogen yield increase from 1 to 3.25±0.4 ( [Formula: see text] ) at pH 4.5 and N(2)-flushing of 58.4 (L·d(-1)). This yield is close to the theoretical acidogenic value (4 [Formula: see text] ). The mechanisms that explain this increase on hydrogen yield shifts are related to the thermodynamics of three metabolic reactions: lactate hydrogenase, NADH hydrogenase and homoacetogenesis, which are affected by the low hydrogen partial pressures.

State indicators for monitoring the anaerobic digestion process.

Anaerobic process state indicators were used to monitor a manure digester exposed to different types of disturbances, in order to find the most proper indicator(s) for monitoring the biogas process. Online indicators tested were biogas production, pH, volatile fatty acids (VFA), and dissolved hydrogen. Offline indicators tested were methane and hydrogen content in the biogas. A CSTR reactor with 7.2 L working volume was operated at a varying hydraulic loading rate (HRT 10-20 days) for 200 days. During this period, the reactor was overloaded with extra organic matter such as glucose, lipid, gelatine, and bio-fibers, in order to create dynamic changes in the process state. Biogas production increased in response to the increase in organic load with a slight decrease in methane content. pH was relatively stable and did not show clear response to hydraulic load changes. However, pH changes were observed in response to extra organic load. Individual VFA concentrations were an effective indicator, with propionate persistent for the longest time after introduction of the disturbance. Dissolved hydrogen was very sensitive to the addition of easily degradable organics. However, it responded also to other disturbances such as slight air exposure which had no impact on process performance. A combination of acetate, propionate and biogas production is an effective combination to monitor this type of digesters effectively.

An innovative online VFA monitoring system for the anerobic process, based on headspace gas chromatography.

A new method for online measurement of volatile fatty acids (VFA) in anerobic digesters has been developed based on headspace gas chromatography (HSGC). The method applies ex situ VFA stripping with variable headspace volume and gas analysis by gas chromatography-flame ionization detection (GC-FID). In each extraction, digester sample was acidified with H(3)PO(4) and NaHSO(4), then heated to strip the VFA into the gas phase. The gas was sampled in a low friction glass syringe before injected into the GC for measurement. The system has been tested for online monitoring of a lab-scale CSTR reactor treating manure for more than 6 months and has shown good agreement with off-line analysis. The system is capable of measuring individual VFA components. This is of advantage since specific VFA components such as propionic and butyric acid can give extra information about the process status. Another important advantage of this sensor is that there is no filtration, which makes possible application in high solids environments. The system can thus be easily applied in a full-scale biogas reactor by connecting the system to the liquid circulation loop to obtain fresh sample from the reactor. Local calibration is needed but automatic calibration is also possible using standard addition method. Sampling duration is 25-40 min, depending on the washing duration, and sensor response is 10 min. This is appropriate for full-scale reactors, since dynamics within most biogas reactors are of the order of several hours.

Effects of process stability on anaerobic biodegradation of LAS in UASB reactors.

Anaerobic biodegradation of linear alkylbenzene sulfonates (LAS) was studied in upflow anaerobic sludge blanket (UASB) reactors operated under mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions. LAS C12 concentration in the influents was 10 mg.L(-1), and the hydraulic retention time in the reactors was 2 days. Adsorption of LAS C12 was assessed in an autoclaved control reactor and ceased after 115 days. The reactors were operated for a minimum of 267 days; 40-80% removal of LAS C12 was observed. A temperature reduction from 55 degrees C to 32 degrees C for 30 h resulted in process imbalance as indicated by increase of volatile fatty acids (VFA). The imbalance was much more intense in the LAS amended reactor compared with an unamended reactor. At the same time, the process imbalance resulted in discontinued LAS removal. This finding indicates that process stability is a key factor in anaerobic biological removal of LAS. After a recovery period, the removal of LAS resumed, providing evidence of biological anaerobic LAS degradation. The removal remained constant until termination of experiments in the reactor. Biodegradation of LAS in the mesophilic reactor was at the same level as in the thermophilic reactor under stable conditions.