Diversity and variability of methanogens during the shift from mesophilic to thermohilic conditions while biogas production

Elucidating the role of sub-thermophilic temperature and pre-hydrolyzation for effective upgrading scheme of old swine manure digesters

Solids concentration, temperature, and digester configuration were subjected to biomethanation study to identify effective retrofitting schemes for old swine waste digesters. Batch assays were commenced to determine an appropriate scenario at 30-55 °C and total solids 1-3 %TS. Sub-thermophilic temperature (45 °C) was found desirable with an additional 11.1 % methane yield, while digestion at higher TS induced ammonium inhibition. Subsequent batch experiments lasted 72 hrs for hydrolytic-acidogenic assessment under various temperatures. Heating control at 45 °C and 55 °C for 24 hrs increased hydrolysis efficiency 4.6-5.7 folds above control but showed no significant difference (α = 0.05) between them. Limited heat supply from biogas engine dictated the continuous digestion study to operate pre-hydrolysis reactor at maximum temperature of 45 °C. The two-stage strategy demonstrated best overall performances at the sub-thermphilic combination, raising methane yield by 35.4 %. Next-Generation Sequencing indicated remarkable shifts in abundance and diversity, especially for hydrolytic organisms, which expanded from 54 to 70.2 % by sub-thermophilic temperature.

Effects of hydrochar and biogas slurry reflux on methane production by mixed anaerobic digestion of cow manure and corn straw

This study aimed to enhance methane production from mixed anaerobic digestion of cow manure and corn straw by adding hydrochar and biogas slurry reflux. The hydrochar characterization revealed that it can provide attachment for microbial growth, and abundant surface functional groups (such as C-O, CO, C-OH, and C-N) for adsorption. Direct interspecies electron transfer (DIET) mediated by surface oxygen-containing functional groups on hydrochar increased the methane yield. The experimental group added with hydrochar and biogas slurry reflux had the highest methane and biogas production (34.40% and 36.98% higher than the control group, respectively). Results demonstrate hydrochar and biogas slurry reflux can improve microorganism species richness in anaerobic digestion systems, in which hydrochar can also improve microorganism species uniformity. Distance-based redundancy analysis showed that the VFAs, and pH had the greatest effects on the composition of the microbial community. The dominant microorganism at the phylum level in AD system were Bacteroidetes, Firmicutes, and Proteobacteria. The addition of hydrochar and biogas slurry reflux can significantly increase the species abundance of Methanobacterium. These results indicate that the addition of hydrochar and biogas slurry reflux can improve the corresponding microbial abundance, in which hydrochar can enhance the redox characteristics and DIET between microorganism, biogas slurry reflux can also increase nutrient content of anaerobic digestion system, and collectively promote the methane yield.

Assessment of Bacterial Diversity of Industrial Poultry Wastewater by Denaturing Gradient Gel Electrophoresis (DGGE) and the Cultivation Method in Order to Inform Its Reuse in Agriculture

Effluents discharged by poultry meat industries are heavily polluted with raw materials, such as fat, blood residues, and proteins. Thus, untreated effluents directly discharged into the environment may constitute a public health threat. This study aims to evaluate the bacterial diversity of three water qualities: industrial poultry wastewater (PWW), tap water (TW), and PWW diluted with TW (50 : 50) (V/V) (TWPWW) by the combination of culture-independent and culture-dependent approaches. The total bacterial DNA was extracted using phenol/chloroform method. The hypervariable 16S rRNA region V3-V5 was amplified by PCR using universal primers. The amplicons were separated by vertical electrophoresis on a polyacrylamide gel of increasing denaturing gradient according to their richness in GC bases. Selected bands were reamplified and sequenced. Pure isolated bacteria from nutrient agar medium were characterized according to their morphological and biochemical characteristics. Genomic DNA from pure strains was extracted by boiling method, and a molecular amplification of the 16S–23S ITS region of the 16S rRNA gene was performed using the universal primers. Selected isolates were identified by sequencing. Results showed a high bacterial load and diversity in PWW in comparison with TW and TWPWW. A collection of 44 strains was obtained, and 25 of them were identified by sequencing. Proteobacteria represented 76% of isolated bacteria Gamma-Proteobacteria was the predominate isolate (68%). Other isolates were Firmicutes (8%), Bacteroidetes (12%), and Actinobacteria (8%). These isolates belong to different genera, namely, Pseudomonas, Acinetobacter, Proteus, Empedobacter, Corynebacterium, Enterobacter, Comamonas, Frondibacter, Leclercia, Staphylococcus, Atlantibacter, Klebsiella, and Microbacterium.

Effects of Stepwise Temperature Shifts in Anaerobic Digestion for Treating Municipal Wastewater Sludge: A Genomic Study

In wastewater treatment plants (WWTP), anaerobic digester (AD) units are commonly operated under mesophilic and thermophilic conditions. In some cases, during the dry season, maintaining a stable temperature in the digester requires additional power to operate a conditioning system. Without proper conditioning systems, methanogens are vulnerable to temperature shifts. This study investigated the effects of temperature shifts on CH₄ gas production and microbial diversity during anaerobic digestion of anaerobic sewage sludge using a metagenomic approach. The research was conducted in lab-scale AD under stepwise upshifted temperature from 42 to 48 °C. The results showed that significant methanogen population reduction during the temperature shift affected the CH₄ production. With 70 days of incubation each, CH₄ production decreased from 4.55 L·g⁻¹-chemical oxygen demand (COD) at 42 °C with methanogen/total population (M·TP⁻¹) ratio of 0.041 to 1.52 L·g⁻¹ COD (M·TP⁻¹ ratio 0.027) and then to 0.94 L·g⁻¹ COD ( M·TP⁻¹ ratio 0.026) after the temperature was shifted to 45 °C and 48 °C, respectively. Methanosaeta was the most prevalent methanogen during the thermal change. This finding suggests that the Methanosaeta genus was a thermotolerant archaea. Anaerobaculum, Fervidobacterium, and Tepidanaerobacter were bacterial genera and grew well in shifted-up temperatures, implying heat-resistant characteristics.

Diversity among activated sludge in vacuum degassed laboratory systems

Vacuum degassing of activated sludge is a technology used to improve sludge settling. By improving the settling ability of the sludge, a higher amount of biomass can be kept in the bioreactor, which further results in better wastewater treatment results. However, the momentaneous vacuum exposition has been found a stress agent for activated sludge flocs and bacteria and may cause changes in sludge activity. However, no biological studies on the long-term intermittent application of vacuum to activated sludge have been published so far. The question arises whether the improvement in the degree of wastewater treatment results from an increase in the amount of biomass involved in the treatment process or does the change in pressure stimulate bacteria to increased activity? The study aimed to examine whether and how cyclic pressure reduction in the biological system affects the activity and composition of bacterial biocenosis of activated sludge. Three sequencing batch reactors were operated for almost three months. The work cycle of two of them included a vacuum degassing stage inserted between reaction and settling stage. Degassing was obtained with a pressure of 300 or 30 hPa. In addition to the wastewater quality analyzes, the microbial activity, number and variety of activated sludge bacteria and the characteristics of activated sludge flocs were determined. There were no significant differences between the reactors in the obtained effects of nutrient removal. All reactors showed organic compounds removal around 93%, and 40% and 58% of nitrogen and phosphorus removal, respectively. Obtained differences in respiratory and dehydrogenase activity were not significant. The biodiversity assessed with DNA sequencing revealed sludge enrichment with unclassified bacteria. Moreover, vacuum degassing caused flocs disintegration. In both the vacuum degassing reactors, the floc size range was much narrower than that of the control sludge. In the sludge degassed with a pressure of 30 hPa, the flocs were 25-80% smaller than in the sludge without the influence of a vacuum. The total number of bacteria was comparable among the reactors, however, in the reactor with degassing pressure of 30 hPa, the share of dead bacteria in the activated sludge (11%) was significantly lower than in other reactors (about 16%). The concentration of extracellular polymers in activated sludge was up to 87% higher when using vacuum degassing of 30 hPa than in other reactors. The results of the presented research show that the changes in the activated sludge occurring under the influence of vacuum degassing do not change the effectiveness of wastewater treatment, but may alter the community composition.

Medium shift influence on nitrogen removal bacteria: Ecophysiology and anammox process performance

In this study, we focused on the proportion of particular bacterial groups and changes in microbial community structure in relation to the anammox process parameters and the feeding medium strategy in the Sequencing Batch Reactor (SBR). In order to present an insight into the microbial dynamics while feeding medium shift from synthetic wastewater to landfill leachate, fluorescent in situ hybridization (FISH), Real Time PCR, PCR - DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) and Reverse Transcription PCR-DGGE analysis were used. Feeding medium change has the strongest impact on relative abundance of denitrifiers and representatives of Planctomycetes. The relative abundancy of specific genes for all investigated nitrogen removal bacterial groups dropped after landfill leachate implementation. However, anammox consortium were able to adapt to the new reactor operating conditions and time for adaptation was estimated at the level of 90 days.

The effect of temperature fluctuation on the microbial diversity and community structure of rural household biogas digesters at Qinghai Plateau

Seasonal temperature-fluctuation has been regarded as a key environmental factor affecting rural biogas fermentation yields. The present study investigated the impact of seasonal temperature-fluctuation on operating-temperatures and biogas production in rural household digesters at Qinghai Plateau and revealed the related changes in microbial diversity and community structure by 16S rRNA gene high-throughput sequencing (HTS) analysis. Our results showed closely positive correlation between operating-temperatures and biogas production. HTS analysis indicated the highest diversity for bacteria community in autumn (at highest operating-temperatures) and late winter (at lowest operating-temperatures) and for archaea community only in autumn. HTS analysis classified bacteria into 21 phyla and 346 genera with the most predominant phyla Firmicutes, Bacteroidetes and Proteobacteria (> 72.4% in total) and the most predominant genera Proteiniphilum, Clostridium sensustricto 1, Petrimonas, Pseudomonas and Fastidiosipila (37.09-38.61% in total). HTS analysis also revealed two main archaea orders (Methanomicrobiales and Methanobacteriales) and one predominant genus Methanogenium to support plateau biogas fermentation. Especially, a remarkable impact of temperature on the community abundances of bacteria phyla Synergistetes and archaea genera Methanogenium and Thermogymnomonas was observed, and such microbial community structure changes were positively consistent with the biogas production. The present work provided the first set of evidences to link temperature-controlled modulation of microbial community structure with rural household biogas production at Qinghai Plateau.

Microbial community composition and methanogens' biodiversity during a temperature shift in a methane fermentation chamber

More information on the connection between anaerobic digestion (AD) parameters and composition of the microbial community involved in the AD process is required to gain a better understanding of how a bioreactor functions. The aim of this study was to analyse the composition of microbial communities and the dynamics of methanogens' biodiversity changes during the shift from mesophilic (38°C) to thermophilic (55°C) conditions during biogas production. The total microbial composition was examined via the metagenomic approach based on 16S rRNA gene sequencing, whereas the methanogen communities were analysed using PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) of mcrA. Even though the temperature is one of the crucial parameters affecting microorganisms involved in the AD process, the results presented here revealed that there were no statistically significant differences in bacterial community composition between the mesophilic and thermophilic phases of the process. The most abundant phyla were found to be Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. However, the methanogens' community genotypic structure as examined by the PCR-DGGE method changed under thermophilic conditions. The temperature had the strongest impact on the archaeal methanogens in the fermentation chamber directly after implementing the temperature shift. A relatively higher biogas yield and average content of CH₄ in the produced biogas were observed under thermophilic conditions.

Cold anammox process and reduced graphene oxide - Varieties of effects during long-term interaction

Because of its energy efficiency, the anaerobic ammonium oxidation (anammox) process has been recognized as the most promising biological nitrogen removal process, but its implementation in mainstream wastewater treatment plants is limited by its relatively high optimal temperature (30 °C). Recently, it was shown that during short-term batch experiments, reduced graphene oxide (RGO) displayed accelerated reaction activity at low temperatures (10-15 °C). In this study, the long-term effects of RGO on the low-temperature anammox process in a sequencing batch reactor (SBR), are studied for the first time, including different methods of interaction. The results presented here show that RGO can stimulate anammox activity up to 17% through two factors: bacterial growth stimulation, which was especially significant at higher temperatures (>15 °C), and an increase of the anammox reaction rate, which occurred only below 15 °C. The bacterial community structure was not influenced by addition of RGO. Moreover, after incubation in an anammox bioreactor, RGO showed signs of degradation and chemical changes as evidenced by the presence of oxygen and calcium on its surface. According to the literature and the obtained results, it is proposed that RGO is oxidized and oxygen is reduced by the organic mediator that is involved in the enzymatic reactions. However, activated sludge is a very complex structure created by numerous, undefined microorganisms, which makes it difficult to determine the exact oxidation mechanism.

Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H2 and CO2 under different temperature conditions

The growth of all methanogens is limited to a specific temperature range. However, Methanothermobacter thermautotrophicus can be found in a variety of natural and artificial environments, the temperatures of which sometimes even exceed the temperature growth ranges of thermophiles. As a result, the extent to which methane production and survival are affected by temperature remains unclear. To investigate the mechanisms of methanogenesis that Archaea have evolved to cope with drastic temperature shifts, the responses of Methanothermobacter thermautotrophicus to temperature were investigated under a high temperature growth (71°C) and cold shock (4°C) using Isobaric tags for relative and absolute quantitation (iTRAQ). The results showed that methane formation is decreased and that protein folding and degradation are increased in both high‐ and low‐temperature treatments. In addition, proteins predicted to be involved in processing environmental information processing and in cell membrane/wall/envelope biogenesis may play key roles in affecting methane formation and enhancing the response of M. thermautotrophicus to temperature stress. Analysis of the genomic locations of the genes corresponding to these temperature‐dependent proteins predicted that 77 of the genes likely to form 32 gene clusters. Here, we assess the response of M. thermautotrophicus to different temperatures and provide a new level of understanding of methane formation and cellular putative adaptive responses.

Biogas Production: Microbiology and Technology

Biogas, containing energy-rich methane, is produced by microbial decomposition of organic material under anaerobic conditions. Under controlled conditions, this process can be used for the production of energy and a nutrient-rich residue suitable for use as a fertilising agent. The biogas can be used for production of heat, electricity or vehicle fuel. Different substrates can be used in the process and, depending on substrate character, various reactor technologies are available. The microbiological process leading to methane production is complex and involves many different types of microorganisms, often operating in close relationships because of the limited amount of energy available for growth. The microbial community structure is shaped by the incoming material, but also by operating parameters such as process temperature. Factors leading to an imbalance in the microbial community can result in process instability or even complete process failure. To ensure stable operation, different key parameters, such as levels of degradation intermediates and gas quality, are often monitored. Despite the fact that the anaerobic digestion process has long been used for industrial production of biogas, many questions need still to be resolved to achieve optimal management and gas yields and to exploit the great energy and nutrient potential available in waste material. This chapter discusses the different aspects that need to be taken into consideration to achieve optimal degradation and gas production, with particular focus on operation management and microbiology.

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

BACKGROUND

Biofuel production from conversion of biomass is indispensable in the portfolio of renewable energies. Complex microbial communities are involved in the anaerobic digestion process of plant material, agricultural residual products and food wastes. Analysis of the genetic potential and microbiology of communities degrading biomass to biofuels is considered to be the key to develop process optimisation strategies. Hence, due to the still incomplete taxonomic and functional characterisation of corresponding communities, new and unknown species are of special interest.

RESULTS

Three mesophilic and one thermophilic production-scale biogas plants (BGPs) were taxonomically profiled using high-throughput 16S rRNA gene amplicon sequencing. All BGPs shared a core microbiome with the thermophilic BGP featuring the lowest diversity. However, the phyla Cloacimonetes and Spirochaetes were unique to BGPs 2 and 3, Fusobacteria were only found in BGP3 and members of the phylum Thermotogae were present only in the thermophilic BGP4. Taxonomic analyses revealed that these distinctive taxa mostly represent so far unknown species. The only exception is the dominant Thermotogae OTU featuring 16S rRNA gene sequence identity to Defluviitoga tunisiensis L3, a sequenced and characterised strain. To further investigate the genetic potential of the biogas communities, corresponding metagenomes were sequenced in a deepness of 347.5 Gbp in total. A combined assembly comprised 80.3 % of all reads and resulted in the prediction of 1.59 million genes on assembled contigs. Genome binning yielded genome bins comprising the prevalent distinctive phyla Cloacimonetes, Spirochaetes, Fusobacteria and Thermotogae. Comparative genome analyses between the most dominant Thermotogae bin and the very closely related Defluviitoga tunisiensis L3 genome originating from the same BGP revealed high genetic similarity. This finding confirmed applicability and reliability of the binning approach. The four highly covered genome bins of the other three distinct phyla showed low or very low genetic similarities to their closest phylogenetic relatives, and therefore indicated their novelty.

CONCLUSIONS

In this study, the 16S rRNA gene sequencing approach and a combined metagenome assembly and binning approach were used for the first time on different production-scale biogas plants and revealed insights into the genetic potential and functional role of so far unknown species.