A balanced microbiota efficiently produces methane in a novel high-rate horizontal anaerobic reactor for the treatment of swine wastewater

The potential and sustainable strategy for swine wastewater treatment: Resource recovery

Swine wastewater is highly polluted with complex and harmful substances that require effective treatment to minimize environmental damage. There are three commonly used biological technologies for treating swine wastewater: conventional biological technology (CBT), microbial electrochemical technology (MET), and microalgae technology (MT). However, there is a lack of comparison among these technologies and a lack of understanding of their unique advantages and efficient operation strategies. This review aims to compare and contrast the characteristics, influencing factors, improvement methods, and microbial mechanisms of each technology. CBT is cost-effective but has low resource recovery efficiency, while MET and MT have the highest potential for resource recovery. However, all three technologies are affected by various factors and toxic substances such as heavy metals and antibiotics. Improved methods include exogenous/endogenous enhancement, series reactor operation, algal-bacterial symbiosis system construction, etc. Though MET is limited by construction costs, CBT and MT have practical applications. While swine wastewater treatment processes have developed automatic control systems, the application need further promotion. Furthermore, key functional microorganisms involved in CBT's pollutant removal or transformation have been detected, as have related genes. The unique electroactive microbial cooperation mode and symbiotic mode of MET and MT were also revealed, respectively. Importantly, the future research should focus on broadening the scope and scale of engineering applications, preventing and controlling emerging pollutants, improving automated management level, focusing on microbial synergistic metabolism, enhancing resource recovery performance, and building a circular economy based on low-cost and resource utilization.

Assessment of cecal microbiota modulation from piglet dietary supplementation with copper

BACKGROUND

Swine production expanded in the last decades. Efforts have been made to improve meat production and to understand its relationship to pig gut microbiota. Copper (Cu) is a usual supplement to growth performance in animal production. Here, two performance studies were conducted to investigate the effects of three different sources of Cu on the microbiota of piglets. A total of 256 weaned piglets were randomly allocated into 4 treatments (10 replicates per treatment of 4 piglets per pen in Trial 1 and 8 replicates of 3 piglets per pen in Trial 2). Treatments included a control group (fed 10 mg/kg of Cu from CuSO₄), a group fed at 160 mg/kg of Copper (II) sulfate (CuSO₄) or tri-basic copper chloride (TBCC), and a group fed with Cu methionine hydroxy analogue chelated (Cu-MHAC) at 150, 80, and 50 mg/kg in Phases 1 (24-35 d), 2 (36-49 d), and 3 (50-70 d), respectively. At 70 d, the cecum luminal contents from one pig per pen were collected and polled for 16 S rRNA sequencing (V3/V4 regions). Parameters were analyzed in a completely randomized block design, in which each experiment was considered as a block.

RESULTS

A total of 1337 Operational Taxonomic Units (OTUs) were identified. Dominance and Simpson ecological metrics were statistically different between control and treated groups (P < 0.10) showing that different Cu sources altered the gut microbiota composition with the proliferation of some bacteria that improve gut health. A high abundance of Prevotella was observed in all treatments while other genera were enriched and differentially modulated, according to the Cu source and dosage. The supplementation with Cu-MHAC can modify a group of bacteria involved in feed efficiency (FE) and short chain fatty acids (SCFA) production (Clostridium XIVa, Desulfovibrio, and Megasphera). These bacteria are also important players in the activation of ghrelin and growth hormones that were previously reported to correlate with Cu-MHAC supplementation.

CONCLUSIONS

These results indicated that some genera seem to be directly affected by the Cu source offered to the animals. TBCC and Cu-MHAC (even in low doses) can promote healthy modifications in the gut bacterial composition, being a promising source of supplementation for piglets.

Complex network analysis of slaughterhouse waste anaerobic digestion: From failure to success of long-term operation

The study explored slaughterhouse waste (SHW) as prime feedstock associated with and without supplement of an external slowly degradable lignocellulosic carbon source to overcome the synergistic co-inhibitions of ammonia and fatty acids. Long-term solid-state digestion (SSD) and liquid-state digestion (LSD) were investigated using a mixture of pork liver and fat. At 2.0 g volatile solids (VS) L^-1 d^-1 of organic loading rate (OLR), the two reactors of SSD experienced operational instability due to ammonia inhibition and volatile fatty acid (VFA) accumulation while LSD successfully produced 0.725 CH₄ L CH₄ g^-1VS during 197 d of working days under unfavorable condition with high total ammonia nitrogen (>4.7 g/L) and VFAs concentration (>1.9 g/L). The network analysis between complex microflora and operational parameters provided an insight for sustainable biogas production using SHW. Among all, hydrogenotrophic methanogens have shown better resistance than acetoclastic methanogens.

Effects of organic loading rates on high-solids anaerobic digestion of food waste in horizontal flow reactor: Methane production, stability and mechanism

To maximize the methane production efficiency of high-solids anaerobic digestion (HSAD) of food waste (FW), a horizontal flow reactor was operated under mesophilic, semi-continuous condition at organic loading rates (OLRs) ranging from 1.00 to 13.80 kg-VS/(m³ d). The gas production, substrate transformation, and microbial community characteristics of the horizontal flow HSAD reactor were evaluated. The results indicated that the methane yield (0.173-0.516 L/(g d)) fluctuated with the increasing OLR, volumetric methane production rate (0.25-5.69 L/(L d)) increased with increasing OLR, and the volatile solids (VS) reduction rate ranged between 83.30% and 93.05%. The relationship of biogas or methane production with OLR and HRT in the horizontal flow HSAD reactor were characterized with an empirical equation. The concentrations of soluble COD and volatile fatty acid exhibited significant fluctuations, and free ammonia-nitrogen peaked at the OLR of 13.80 kg-VS/(m³ d). Microbial community analysis revealed that the methanogenic metabolic pathway changes along the propelling direction of the horizontal flow HSAD reactor from CH₃COOH and H₂/CO₂ pathways to CH₃COOH, H₂/CO₂, and H₂/methyl co-dominant pathways. These results provide theoretical support for stable methane production from FW and deeper insight into horizontal flow HSAD for FW treatment.

Effect of microaerophilic treatment on swine wastewater (SWW) treatment: Engineering and microbiological aspects

The microaerobic process on swine wastewater (SWW) treatment was investigated, evaluating its effect on organic matter hydrolysis and removal, biogas production, operational stability, and microbial community structure. UASB reactors operating under higher organic loading rates (OLRs) and lower hydraulic retention times (HRTs) than those found in the SWW treatment literature were also assessed. The microaerophilic reactor R2 presented a higher total and particulate organic matter removals and operational stability than the anaerobic reactor R1, reaching COD_P removals of 79.4 ± 4.6%. In the specific methanogenic activity (SMA) tests, the microaerobic sludge (R2) showed hydrolytic and acetogenic/methanogenic activity superior to inoculum and anaerobic sludge (R1). The microbiological evaluation of R2 revealed the high presence of hydrolytic microorganisms, therefore justifying the higher hydrolytic activity found in the SMA tests and higher particulate organic matter removal found in the microaerobic reactor.

Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry

Anaerobic digestion can produce biogas as an eco-friendly energy source, driven by a microbial community-dependent process and, as such, suffer influences from many biotic and abiotic factors. Understanding the players and how they interact, the mechanisms involved, what the factors are, and how they influence the biogas process and production is an important way to better control it and make it more efficient. Metagenomic approach is a powerful tool to assess microbial diversity and further, allow correlating changes in microbial communities with multiple factors in virtually all environments. In the present study, we used metagenomic approach to assess microbial community structure changes in two biodigesters, differing in their biogas production capacity, architecture, and feed. A total of 1,440,096 reads of the 16S rRNA gene V4 region were obtained and analyzed. The main bacterial phyla were Firmicutes and Bacteroidetes in both biodigesters, but the biodiversity was greater in the Upflow Anaerobic Sludge Blanket (UASB) reactor fed with bovine manure than in the Continuous Stirred Tank Reactor (CSTR) fed with swine manure, which also correlated with an increase in biogas or methane production. Microbial community structure associated with biodigesters changed seasonally and depended on animal growth stage. Random forest algorithm analysis revealed key microbial taxa for each biodigester. Candidatus Cloacomonas, Methanospirillum, and Methanosphaera were the marker taxa for UASB and the archaea groups Methanobrevibacter and Candidatus Methanoplasma were the marker taxa for CSTR. A high abundance of Candidatus Methanoplasma and Marinimicrobia SAR406 clade suggested lower increments in methane production. Network analysis pointed to negative and positive associations and specific key groups, essential in maintaining the anaerobic digestion (AD) process, as being uncultured Parcubacteria bacteria, Candidatus Cloacomonas, and Candidatus Methanoplasma groups, whose functions in AD require investigation.

Modeling anaerobic digestion metabolic pathways for antibiotic-contaminated wastewater treatment

Anaerobic digestion has been used to treat antibiotic-contaminated wastewaters. However, it is not always effective, since biodegradation is the main removal mechanism and depends on the compound chemical characteristics and on how microbial metabolic pathways are affected by the reactor operational conditions and hydrodynamic characteristics. The aim of this study was to develop a mathematical model to describe 16 metabolic pathways of an anaerobic process treating sulfamethazine-contaminated wastewater. Contois kinetics and a useful reaction volume term were used to represent the biomass concentration impact on bed porosity in a N continuously stirred tank modeling approach. Two sulfamethazine removal hypotheses were evaluated: an apparent enzymatic reaction and a cometabolic degradation. Additionally, long-term modeling was developed to describe how the operational conditions affected the performance of the process. The best degradation correlations were associated with the consumption of carbohydrates, proteins and it was inversely related to acetic acid production during acidogenesis.

Recent advancement on biological technologies and strategies for resource recovery from swine wastewater

Swine wastewater is categorized as one of the agricultural wastewater with high contents of organics and nutrients including nitrogen and phosphorus, which may lead to eutrophication in the environment. Insufficient technologies to remove those nutrients could lead to environmental problems after discharge. Several physical and chemical methods have been applied to treat the swine wastewater, but biological treatments are considered as the promising methods due to the cost effectiveness and performance efficiency along with the production of valuable products and bioenergies. This review summarizes the characteristics of swine wastewaters in the beginning, and briefly describes the current issues on the treatments of swine wastewaters. Several biological techniques, such as anaerobic digestion, A/O process, microbial fuel cells, and microalgae cultivations, and their future aspects will be addressed. Finally, the potentials to reutilize biomass produced during the treatment processes are also presented under the consideration of circular economy.

Characterisation and microbial community analysis of lipid utilising microorganisms for biogas formation

In the anaerobic process, fat-oil-grease (FOG) is hydrolysed to long-chain fatty acids (LCFAs) and glycerol (GLYC), which are then used as substrates to produce biogas. The increase in FOG and LCFAs inhibits methanogenesis, and so far, most work investigating this inhibition has been carried out when FOG or LCFAs were used as co-substrates. In the current work, the inhibition of methanogenesis by FOG, LCFAs and GLYC was investigated when used as sole substrates. To gain more insight on the dynamics of this process, the change of microbial community was analysed using 16S rRNA gene amplicon sequencing. The results indicate that, as the concentrations of cooking olive oil (CO, which represents FOG) and LCFAs increase, methanogenesis is inhibited. For instance, at 0.01 g. L-1 of FOG, the rate of biogas formation was around 8 ml.L-1.day-1, and this decreased to <4 ml.L-1.day-1 at 40 g.L-1. Similar results were observed with the use of LCFAs. However, GLYC concentrations up to 100g.L-1 did not affect the rate of biogas formation. Acidic pH, temperature > = 45°C and NaCl > 3% led to a significant decrease in the rate of biogas formation. Microbial community analyses were carried out from samples from 3 different bioreactors (CO, OLEI and GLYC), on day 1, 5 and 15. In each bioreactor, microbial communities were dominated by Proteobacteria, Firmicutes and Bacteroidetes phyla. The most important families were Enterobacteriaceae, Pseudomonadaceae and Shewanellaceae (Proteobacteria phylum), Clostridiacea and Ruminococcaceae (Firmicutes) and Porphyromonadaceae and Bacteroidaceae (Bacteroidetes). In CO bioreactor, Proteobacteria bacteria decreased over time, while those of OLEI and GLYC bioreactors increased. A more pronounced increase in Bacteroidetes and Firmicutes were observed in CO bioreactor. The methanogenic archaea Methanobacteriaceae and Methanocorpusculaceae were identified. This analysis has shown that a set of microbial population is selected as a function of the substrate.

Predominance of syntrophic bacteria, Methanosaeta and Methanoculleus in a two-stage up-flow anaerobic sludge blanket reactor treating coffee processing wastewater at high organic loading rate

The effect of the organic loading rate (OLR) on the performance and microbial composition of a two-stage UASB system treating coffee processing wastewater was assessed. The system was operated with OLR up to 18.2 g COD (L d)^-1 and effluent recirculation. Methane production and effluent characteristics were monitored. The microbial composition was examined through next-generation sequencing and qPCR from the anaerobic sludge of the first reactor (R1) operated at low and high OLR. The system showed operational stability, obtaining a maximum methane production of 2.2 L CH₄ (L d)^-1, with a removal efficiency of COD and phenolic compounds of 84 and 73%, respectively. The performance of R1 at high OLR in steady conditions was associated with an appropriate proportion of nutrients (particularly Fe) and a marked increase of the syntrophic bacteria Syntrophus and Candidatus Cloacimonas, and acetoclastic and hydrogenotrophic methanogens, mainly Methanosaeta, Methanoculleus, Methanobacterium and Methanomassiliicoccus.

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis. This negligence was mainly due to the lack of knowledge regarding the biases influencing specific steps of the microbiome investigation process. In the present study, the main technical aspects of the 16S rRNA analysis were checked giving special attention to the approach used for high throughput sequencing. More specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing and shotgun DNA underestimated the Methanoculleus genus, probably due to the low 16S rRNA gene copy number encoded in this taxon.

Removal of the veterinary antimicrobial sulfamethazine in a horizontal-flow anaerobic immobilized biomass (HAIB) reactor subjected to step changes in the applied organic loading rate

A bench-scale horizontal-flow anaerobic immobilized biomass (HAIB) reactor treating synthetic swine wastewater was operated under different applied organic loading rates (OLR) through both variations in feed strength and in hydraulic retention time (HRT). The influence of step changes in OLR on the removal of the veterinary antimicrobial sulfamethazine (SMZ) was assessed. The highest observed SMZ removal efficiency, 75 ± 6%, was achieved with an OLR of 2.7 ± 0.4 kg O₂ m^-3 d^-1 when a significant increase in COD removal rate was observed. The SMZ removal rate was positively correlated (r = 0.899) to the COD removal rate in all of the experimental conditions in which the HRT was kept at 24 h, indicating a cometabolic transformation of the antimicrobial. Decreasing the HRT caused a significant decrease in SMZ removal efficiency without affecting the HAIB reactor performance in terms of stability, COD removal or metabolic intermediates production. Functionally equivalent steady states were observed in four different operational phases with similar operating conditions but with widely different behavior in relation to SMZ removal. The experimental results showed the potential of anaerobic technology in removing environmentally relevant concentrations of SMZ, and the possibility of enhancing reactor performance by controlling operating conditions.

Improved methane production from sugarcane vinasse with filter cake in thermophilic UASB reactors, with predominance of Methanothermobacter and Methanosarcina archaea and Thermotogae bacteria

Biogas production from sugarcane vinasse has enormous economic, energy, and environmental management potential. However, methane production stability and biodigested vinasse quality remain key issues, requiring better nutrient and alkalinity availability, operational strategies, and knowledge of reactor microbiota. This study demonstrates increased methane production from vinasse through the use of sugarcane filter cake and improved effluent recirculation, with elevated organic loading rates (OLR) and good reactor stability. We used UASB reactors in a two-stage configuration, with OLRs up to 45gCODL^-1d^-1, and obtained methane production as high as 3LL^-1d^-1. Quantitative PCR indicated balanced amounts of bacteria and archaea in the sludge (10⁹-10¹⁰copiesg^-1VS), and of the predominant archaea orders, Methanobacteriales and Methanosarcinales (10⁶-10⁸copiesg^-1VS). 16S rDNA sequencing also indicated the thermophilic Thermotogae as the most abundant class of bacteria in the sludge.

Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge

BACKGROUND

Improved carbohydrate-active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals, and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs a unique niche to look for CAZymes that can potentiate the enzyme blends currently used in industry.

RESULTS

Enzymatic assays showed that functional CAZymes were secreted into the AD environments in four full-scale mesophilic Danish ADs fed with primary and surplus sludge from municipal wastewater treatment plants. Metagenomes from the ADs were mined for CAZymes with Homology to Peptide Patterns (HotPep). 19,335 CAZymes were identified of which 30% showed 50% or lower identity to known proteins demonstrating that ADs make up a promising pool for discovery of novel CAZymes. A function was assigned to 54% of all CAZymes identified by HotPep. Many different α-glucan-acting CAZymes were identified in the four metagenomes, and the most abundant family was glycoside hydrolase family 13, which contains α-glucan-acting CAZymes. Cellulytic and xylanolytic CAZymes were also abundant in the four metagenomes. The cellulytic enzymes were limited almost to endoglucanases and β-glucosidases, which reflect the large amount of partly degraded cellulose in the sludge. No dockerin domains were identified suggesting that the cellulytic enzymes in the ADs studied operate independently. Of xylanolytic CAZymes, especially xylanases and β-xylosidase, but also a battery of accessory enzymes, were present in the four ADs.

CONCLUSIONS

Our findings suggest that the ADs are a good place to look for novel plant biomass degrading and modifying enzymes that can potentiate biological processes and provide basis for production of a range of added-value products from biorefineries.

Anaerobic co-digestion of vegetable waste and swine wastewater in high-rate horizontal reactors with fixed bed

Considering the high waste generation that comes from agriculture and livestock farming, as well as the demand for natural gas, it is necessary to develop sustainable technologies which can reduce environmental impact. There is no available literature on the use of high-rate horizontal anaerobic reactors with fixed bed (HARFB) and continuous feed for the co-digestion of vegetable wastes (VW) and swine wastewater (SW). The aim of this work was to evaluate the reactor performance in terms of methane production, organic matter consumption, and removal of total and thermotolerant coliforms under different proportions of SW and VW, and organic loading rates (OLR) of 4.0, 5.2 and 11.0g COD (Ld)(-)(1). The mixture of SW and VW in the proportions of 90:10, 80:20 and 70:30 (SW:VW) with those OLRs provided great buffering capacity, with partial alkalinity reaching 3552mgL(-1), thereby avoiding the inhibition of methane production by volatile fatty acids produced during the fermentation process. Higher proportions of VW and higher OLR improved volumetric methane production with a maximum value of 1.08LCH4 (Ld)(-)(1), organic matter removal rates up to 98% and total and thermotolerant coliform removal rates of 99% were also observed.

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

BACKGROUND

Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge.

RESULTS

In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway.

CONCLUSION

This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.