Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing

Insight into physico-chemical properties and microbial community structure of biogas slurry from household biogas plants of sub-Himalaya for its implications in improved biogas production

Numerous metagenomics studies, conducted in both full-scale anaerobic digesters and household biogas plants, have shed light on the composition and activity of microbial flora essential for optimizing the performance of biogas reactors, underscoring the significance of microbial community composition in biogas plant efficiency. Although the efficiency of household biogas plants in the sub-Himalayan region has been reported, there is no literature evidence on the microbial community structure of such household biogas plants in the sub-Himalayan region. The current study evaluated the physico-chemical properties and bacterial community structure from the slurry samples of household biogas plants prevalent in the sub-Himalayan region. The slurry samples were observed to be rich in nutrients; however, their carbon and nitrogen contents were higher than the recommended standard values of liquid-fermented organic manure. The species richness and diversity indices (Chao1, Shannon, and Simpson) of household biogas plants were quite similar to the advanced biogas reactors operating at mesophilic conditions. 16S rRNA gene amplicon sequencing reveals microbial diversity, showing a higher abundance of Firmicutes (70.9%) and Euryarchaeota (9.52%) in advanced biogas reactors compared to household biogas plants. Microbial analysis shows a lack of beneficial microbes for anaerobic digestion, which might be the reason for inefficient biogas production in household biogas plants of the sub-Himalayan region. The lack of efficient bacterial biomass may also be attributed to the digester design, feedstock, and ambient temperatures. This study emphasized the establishment of efficient microbial consortia for enhanced degradation rates that may increase the methane yield in biogas plants.

Metagenomic insights into plasmid-mediated antimicrobial resistance in poultry slaughterhouse wastewater: antibiotics occurrence and genetic markers

Slaughterhouse wastewater represents important convergence and concentration points for antimicrobial residues, bacteria, and antibiotic resistance genes (ARG), which can promote antimicrobial resistance propagation in different environmental compartments. This study reports the assessment of the metaplasmidome-associated resistome in poultry slaughterhouse wastewater treated by biological processes, employing metagenomic sequencing. Antimicrobial residues from a wastewater treatment plant (WWTP) that treats poultry slaughterhouse influents and effluents were investigated through high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS). Residues from the macrolide, sulfonamide, and fluoroquinolone classes were detected, the latter two persisting after the wastewater treatment. The genetic markers 16S rRNA rrs (bacterial community) and uidA (Escherichia coli) were investigated by RT-qPCR and the sul1 and int1 genes by qPCR. After treatment, the 16S rRNA rrs, uidA, sul1, and int1 markers exhibited reductions of 0.67, 1.07, 1.28, and 0.79 genes copies, respectively, with no statistical significance (p > 0.05). The plasmidome-focused metagenomics sequences (MiSeq platform (Illumina®)) revealed more than 100 ARG in the WWTP influent, which can potentially confer resistance to 14 pharmacological classes relevant in the human and veterinary clinical contexts, in which the qnr gene (resistance to fluoroquinolones) was the most prevalent. Only 7.8% of ARG were reduced after wastewater treatment, and the remaining 92.2% were associated with an increase in the prevalence of ARG linked to multidrug efflux pumps, substrate-specific for certain classes of antibiotics, or broad resistance to multiple medications. These data demonstrate that wastewater from poultry slaughterhouses plays a crucial role as an ARG reservoir and in the spread of AMR into the environment.

Anaerobic co-metabolic biodegradation of pharmaceuticals and personal care products driven by glycerol fermentation

Anaerobic digestion in two sequential phases, acidogenesis and methanogenesis, has been shown to be beneficial for enhancing the biomethane generation from wastewater. In this work, the application of glycerol (GOH) as a fermentation co-substrate during the wastewater treatment was evaluated on the biodegradation of different pharmaceuticals and personal care products (PPCPs). GOH co-digestion during acidogenesis led to a significant increase in the biodegradation of acetaminophen (from 78 to 89%), ciprofloxacin (from 25 to 46%), naproxen (from 73 to 86%), diclofenac (from 36 to 48%), ibuprofen (from 65 to 88%), metoprolol (from 45 to 59%), methylparaben (from 64 to 78%) and propylparaben (from 68 to 74%). The heterotrophic co-metabolism of PPCPs driven by glycerol was confirmed by the biodegradation kinetics, in which kbio (biodegradation kinetics constant) values increased from 0.18 to 2.11 to 0.27-3.60 L g-1-VSS d-1, for the operational phases without and with GOH, respectively. The assessment of metabolic pathways in each phase revealed that the prevalence of aromatic compounds degradation, metabolism of xenobiotics by cytochrome P450, and benzoate degradation routes during acidogenesis are key factors for the enzymatic mechanisms linked to the PPCPs co-metabolism. The phase separation of anaerobic digestion was effective in the PPCPs biodegradation, and the co-fermentation of glycerol provided an increase in the generation potential of biomethane in the system (energetic potential of 5.0 and 6.3 kJ g-1-CODremoved, without and with GOH, respectively). This study showed evidence that glycerol co-fermentation can exert a synergistic effect on the PPCPs removal during anaerobic digestion mediated by heterotrophic co-metabolism.

Microbial and functional characterization of granulated sludge from full-scale UASB thermophilic reactor applied to sugarcane vinasse treatment

Considering the scarcity of data in the literature regarding phylogenetic and metabolic composition of different inocula, especially those from thermophilic conditions, this research aimed at characterizing the microbial community and preferable metabolic pathways of an UASB reactor sludge applied to the thermophilic treatment (55°C) of sugarcane vinasse, by means of shotgun metagenomics. After its metabolic potential was depicted, it was possible to observe several genes encoding enzymes that are of great importance to anaerobic digestion processes with different wastes as substrate, especially regarding the biodegradation of carbohydrates and ligninolytic compounds, glycerolypids, volatile fatty acids and alcohols metabolism and biogas (H2 and CH4) production. The genera identified in higher relative abundances for Bacteria domain were Sulfirimonas (37.52 ± 1.8%), possibly related to the sludge endogenic activity due to its strong relation with a peptidoglycan lyase enzymes family, followed by Fluviicola (5.01 ± 1.0%), Defluviitoga (4.36 ± 0.2%), Coprothermobacter (4.32 ± 0.5%), Fervidobacterium (2.93 ± 0.3%), Marinospirillum (2.75 ± 0.2%), Pseudomonas (2.14 ± 0.2%) and Flavobacterium (1.78 ± 0.1%), mostly related with carbohydrates fermentations and/or H2 production. For Archaea domain, Methanosarcina (0.61 ± 0.1%), Methanothermobacter (0.38 ± 0.0%), Methanoculleus (0.30 ± 0.1%), Thermococcus (0.03 ± 0.0%), Methanolobus (0.02 ± 1.8%), Methanobacterium (0.013 ± 0.0%), Aciduliprofundum and Pyrococcus (0.01 ± 0.0%) were the most dominant ones, being Methanosarcina the most related with methanogenesis. It was concluded that the robust inoculum description performed in this study may subside future biotechnological researches by using similar inocula (UASB sludges), focusing on the obtainment of value-added by-products by means of anaerobic digestion, such as volatile fatty acids, alcohols and biogas (H2 and CH4), by using several types of waste as substrate.

Two problems in one shot: Vinasse and glycerol co-digestion in a thermophilic high-rate reactor to improve process stability even at high sulfate concentrations

Anaerobic co-digestion (AcoD) of sugarcane vinasse and glycerol can be profitable because of the destination of two biofuel wastes produced in large quantities in Brazil (ethanol and biodiesel, respectively) and the complementary properties of these substrates. Thus, the objective of this study was to assess the effect of increasing the organic loading rate (OLR) from 2 to 20 kg COD m^-3 d^-1 on the AcoD of vinasse and glycerol (50 %:50 % on a COD basis) in a thermophilic (55 °C) anaerobic fluidized bed reactor (AFBR). The highest methane production rate was observed at 20 kg COD m^-3 d^-1 (8.83 L CH₄ d^-1 L^-1), while the methane yield remained stable at around 265 NmL CH₄ g^-1 COD_rem in all conditions, even when influent vinasse reached 1811 mg SO₄^2- L^-1 (10 kg COD m^-3 d^-1). Sulfate was not detected in the effluent. Bacterial genera related to sulfate removal, such as Desulfovibrio and Desulfomicrobium, were observed by means of shotgun metagenomic sequencing at 10 kg COD m^-3 d^-1, as well as the acetoclastic archaea Methanosaeta and prevalence of genes encoding enzymes related to acetoclastic methanogenesis. It was concluded that process efficiency and methane production occurred even in higher sulfate concentrations due to glycerol addition.

Inoculum-to-substrate ratio and solid content effects over in natura spent coffee grounds anaerobic digestion

Coffee is the second most traded commodity worldwide, and its production is associated with the generation of a large number of residues, which are underused and disposed of in landfills. Notably, the coffee industry annually generates approximately 6 million tons of industrial spent coffee ground (ISCG) when extracting coffee flavorings to produce soluble coffee. That resource loss scenario has been highlighted in sustainable waste management contexts as an opportunity to improve the coffee circular economy. Despite ISCG bioconversion to methane potentially meets the waste-to-energy purposes of reducing residues disposal in landfills, decreasing greenhouse gas (GHG) emissions, and increasing renewable energy sources, data about anaerobic digestion (AD) of ISCG remains quite restricted. That limitation becomes more apparent owing to the lack of data focusing on AD key parameters for ISCG as substrate. This study assessed the influence of inoculum-to-substrate ratio (ISR) and the solid content influences on mesophilic (37 °C) ISCG-AD throughout the Response Surface Methodology (RSM) and Central Composite Design (CCD). Results revealed that both factors, ISR and solid content, should be kept above a certain threshold of 0.5 and 6.0 gTVS L^-1 to ensure experimental reliability, as well as reproductively and above 1.0 and 8.0 gTVS L^-1 to avoid underestimation on the MY potential achieved. Concerning ISCG-AD kinetics, the quadratic model optimum condition was at 1.36 and 14.83 gTVS L^-1 for ISR and solid content, respectively. This optimum range for ISR and solid content could guide further development of process configurations for mono- and co-digestion of ISCG, avoiding underestimation of the MY potential and extended incubation periods.

Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil

Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.

Biogas production and nutrients removal from slaughterhouse wastewater using integrated anaerobic and aerobic granular intermittent SBRs - Bioreactors stability and microbial dynamics

Slaughterhouse wastewater (SWW) was effectively treated in sequential anaerobic and aerobic granular intermittent sequencing batch reactors (ASBR+ISBR) for 665 days at different HRTs (48 h, 32 h, 24 h, and 12 h). The ASBR was stable at each HRT but performed relatively well at 12 h (OLR - 7.8-9.8 kg COD/m³-d) in terms of pollutants removal and biogas production than previously conducted research. The average biogas production was about 17.3 L/day having 70-76 % of CH₄ which could subsidize around 52 % of electricity demand while saving 103 US dollars/day if installed at full scale. In the case of post aerobic granular ISBR, carbon and nutrients removal (N&P) was achieved by enriching granules (1.7-2.2 mm) at low DO (0.5-0.8 mg/L) via the nitrite pathway. The ISBR was also well stable at 12 h HRT (average OLR of 2.1 kg COD/m³-d) and met the effluent discharge guidelines recommended by the Central Pollution Control Board of India. During steady-state conditions (12 h HRT), the average removal efficiencies for COD, TSS, O&G, TN, and PO₄-P were 98.8 %, 96.4 %, 98.7 %, 93.4 %, and 86.6 % respectively from combined ASBR and ISBR. The microbial analysis confirmed Euryarchaeota, Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Planctomycetes, and Synergistetes as the dominant phyla in ASBR. Methanosaeta (21.56 %) and Methanosarcina (6.48 %) were the prevailing methanogens for CH₄ production. The leading phyla observed in ISBR were Bacteroidetes, Proteobacteria, Firmicutes, Armatimonadetes, Verrucomicrobia, Chloroflexi, and Planctomycetes. Heterotrophic AOB (Thauera, Xanthomonadaceae, Pseudomonas, Sphingomonadaceae, and Rhodococcus) were mainly detected in the system for ammonia oxidation besides common autotrophic AOB. Similarly, a known PAO (Accumulibacter) was not identified but other PAO (Rhodocyclaceae, Dechloromonas, Pseudomonas, Flavobacteriaceae, and Sphingobacteriaceae) were prevalent inside aerobic granular ISBR that contributed to both carbon and nutrients removal. The results obtained would help implement the investigated reactor configurations at the pilot and full scale for SWW treatment.

Microbiological insights into anaerobic digestion for biogas, hydrogen or volatile fatty acids (VFAs): a review

In the past decades, considerable attention has been directed toward anaerobic digestion (AD), which is an effective biological process for converting diverse organic wastes into biogas, volatile fatty acids (VFAs), biohydrogen, etc. The microbial bioprocessing takes part during AD is of substantial significance, and one of the crucial approaches for the deep and adequate understanding and manipulating it toward different products is process microbiology. Due to highly complexity of AD microbiome, it is critically important to study the involved microorganisms in AD. In recent years, in addition to traditional methods, novel molecular techniques and meta-omics approaches have been developed which provide accurate details about microbial communities involved AD. Better understanding of process microbiomes could guide us in identifying and controlling various factors in both improving the AD process and diverting metabolic pathway toward production of selective bio-products. This review covers various platforms of AD process that results in different final products from microbiological point of view. The review also highlights distinctive interactions occurring among microbial communities. Furthermore, assessment of these communities existing in the anaerobic digesters is discussed to provide more insights into their structure, dynamics, and metabolic pathways. Moreover, the important factors affecting microbial communities in each platform of AD are highlighted. Finally, the review provides some recent applications of AD for the production of novel bio-products and deals with challenges and future perspectives of AD.

Assessing the Influence of Electrode Polarity on the Treatment of Poultry Slaughterhouse Wastewater

Electrochemical methods have been increasingly gaining popularity in the field of wastewater treatment. However, the performance of these methods can be highly affected by the polarity direction as determined by the electrodes arrangement (anode to cathode or cathode to anode); as well as the characteristics of the wastewater to be treated as determined by the type of wastewater. The presented research work investigated the relationship between polarity direction and the removal of pollutants from poultry slaughterhouse wastewater using titanium and aluminium electrode materials. In the first case, the wastewater was exposed to the Ti (anode)-Al (cathode) combination, whereas in the second case the wastewater was subjected to the Al (anode)-Ti (cathode) arrangement. The two cases were designed to see if the polarity direction of the chosen electrode materials affected the removal of pollutants. The removal efficiencies were computed as a ratio of the remaining concentration in the treated effluent to the concentration before treatment. It was observed that the production processes generate highly fluctuating wastewater in terms of pollution loading; for instance, 422 to 5340 Pt-Co (minimum to maximum) were recorded from color, 126 to 2264 mg/L were recorded from total dissolved solids, and 358 to 5998 mg/L from chemical oxygen demand. Also, the research results after 40 min of retention time showed that both electrode arrangements achieved relatively high removal efficiencies; Whereby, the aluminium to titanium polarity achieved up to 100% removal efficiency from turbidity while the titanium to aluminium polarity achieved a maximum of 99.95% removal efficiency from turbidty. Also, a similar phenomenon was observed from total dissolved solids; whereby, on average 0 mg/L was achieved when the wastewater was purified using the aluminium to titanium arrangement, while on average 2 mg/L was achieved from the titanium to aluminium arrangement. A little higher removal efficiency discrepancy was observed from ammonia; whereby, the aluminium to titanium arrangement outperformed the titanium to aluminium arrangement with average removal efficiencies of 82.27% and 64.11%, respectively.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Enhancing a Transition to a Circular Economy in the Water Sector: The EU Project WIDER UPTAKE

Wastewater treatment plants (WWTPs) require an urgent transition from a linear to a circular economy operation/design concept with a consequent resource recovery and more sustainable waste management. Natural resources have to be preserved, and wastes have to become an opportunity for recovering resources and materials (water reuse, energy, sludge reuse). However, the transition toward a circular economy is a complex and long process due to the existence of technical, economic, social and regulatory barriers. These existing barriers are critical challenges for a modern and sustainable WWTP concept. The recovery of resources must be considered a strategic target from the earliest process-design phase. In this context, the European Union’s Horizon 2020 project “Achieving wider uptake of water-smart solutions—WIDER UPTAKE” aims to overcome the existing barriers (technological, regulatory, organizational, social and economic) toward the transition from a linear to a circular economy model for WWTPs. This study is aimed at increasing the awareness of the existing barriers to a circular economy and summarizes the key contributions of the WIDER UPTAKE project in terms of water reuse, sludge reuse and nutrient recovery.

Microbial Diversity Dynamics in a Methanogenic-Sulfidogenic UASB Reactor

In this study, the long-term performance and microbial dynamics of an Upflow Anaerobic Sludge Blanket (UASB) reactor targeting sulfate reduction in a SOx emissions treatment system were assessed using crude glycerol as organic carbon source and electron donor under constant S and C loading rates. The reactor was inoculated with granular sludge obtained from a pulp and paper industry and fed at a constant inlet sulfate concentration of 250 mg S-SO₄²⁻L⁻¹ and a constant C/S ratio of 1.5 ± 0.3 g Cg⁻¹ S for over 500 days. Apart from the regular analysis of chemical species, Illumina analyses of the 16S rRNA gene were used to study the dynamics of the bacterial community along with the whole operation. The reactor was sampled along the operation to monitor its diversity and the changes in targeted species to gain insight into the performance of the sulfidogenic UASB. Moreover, studies on the stratification of the sludge bed were performed by sampling at different reactor heights. Shifts in the UASB performance correlated well with the main shifts in microbial communities of interest. A progressive loss of the methanogenic capacity towards a fully sulfidogenic UASB was explained by a progressive wash-out of methanogenic Archaea, which were outcompeted by sulfate-reducing bacteria. Desulfovibrio was found as the main sulfate-reducing genus in the reactor along time. A progressive reduction in the sulfidogenic capacity of the UASB was found in the long run due to the accumulation of a slime-like substance in the UASB.

Analysis of Microbial Communities and Pathogen Detection in Domestic Sewage Using Metagenomic Sequencing

Wastewater contains diverse microbes, and regular microbiological screening at wastewater treatment plants is essential for monitoring the wastewater treatment and protecting environmental health. In this study, a metagenomic approach was used to characterize the microbial communities in the influent and effluent of a conventional domestic sewage treatment plant in the metropolitan city of Jeddah. Bacteria were the prevalent type of microbe in both the influent and effluent, whereas archaea and viruses were each detected at <1% abundance. Greater diversity was observed in effluent bacterial populations compared with influent, despite containing similar major taxa. These taxa consisted primarily of Proteobacteria, followed by Bacteroidetes and Firmicutes. Metagenomic analysis provided broad profiles of 87 pathogenic/opportunistic bacteria belonging to 47 distinct genera in the domestic sewage samples, with most having <1% abundance. The archaea community included 20 methanogenic genera. The virus-associated sequences were classified mainly into the families Myoviridae, Siphoviridae, and Podoviridae. Genes related to resistance to antibiotics and toxic compounds, gram-negative cell wall components, and flagellar motility in prokaryotes identified in metagenomes from both types of samples. This study provides a comprehensive understanding of microbial communities in influent and effluent samples of a conventional domestic sewage treatment plant and suggests that metagenomic analysis is a feasible approach for microbiological monitoring of wastewater treatment.

Removal of TCOD and phosphate from slaughterhouse wastewater using Fenton as a post-treatment of an UASB reactor

A pilot was designed to study the removal efficiencies of total chemical oxygen demand (TCOD) and phosphate by a combined biological and chemical method. Two stages of Up-flow anaerobic sludge blanket (UASB) reactor and advanced oxidation processes was operated in batch mode. The UASB reactor was operated with hydraulic retention time of 26 h. UASB removal efficiency of TCOD and phosphate were 62.2 and 36.5%, respectively. Fenton process was used as a post-treatment so as to remove organic matter and nutrients. At this stage, the removal efficiencies of TCOD and phosphate were investigated considering the effect of parameters such as pH, hydrogen peroxide and Fe (II) dose based on Taguchi experimental design. Accordingly, under optimum conditions, pH = 3, 1000 mg/l of H₂O₂ and 400 mg/l of Fe (II) the removal efficiencies of TCOD and phosphate reached 95.41 and 85.29%, respectively. The combined method removed TCOD and phosphate up to 98.6 and 90.5%, respectively.

Influence of organic loading rate on ciprofloxacin and sulfamethoxazole biodegradation in anaerobic fixed bed biofilm reactors

Antibiotic compounds, notably sulfamethoxazole (SMX) and ciprofloxacin (CIP), are ubiquitous emerging contaminants (ECs), which are often found in domestic sewage. They are associated with the development of antimicrobial resistance. Operational parameters, e.g. organic loading rate (OLR), hydraulic retention time (HRT) and sludge retention time, may influence EC biodegradation in wastewater treatment plants. This study assessed the impact of the OLR variation on the biodegradation of CIP and SMX, applying two configurations of anaerobic fixed bed reactors: anaerobic packed bed biofilm reactor (APBBR) and anaerobic structured bed biofilm reactor (ASBBR). A significant reduction in the biodegradation of SMX (APBBR: 93-69%; ASBBR: 94-81%) and CIP (APBBR: 85-66%; ASBBR: 85-64%) was observed increasing OLR from 0.6 to 2.0 kgCOD m^-3 d^-1. The decrease in the HRT from 12 to 4 h resulted in higher liquid-phase mass transfer coefficient (APBBR: k_s from 0.01 to 0.05 cm h^-1; ASBBR: k_s from 0.07 to 0.24 cm h^-1), but this was not enough to overcome the decrease in the antibiotic-biomass contact time on biofilm, thus reducing the bioreactors' performance. The ASBBR favored biomethane production (from 7 to 17 mLCH₄ g^-1VSS L^-1 d^-1) and biodegradation kinetics (k_bio from 1.7 to 4.2 and for SMX and from 2.1 to 4.8 L g^-1VSS d^-1 for CIP) due to the higher relative abundance of the archaea community in the biofilm and the lower liquid-phase mass transfer resistance in the structured bed. CIP and SMX cometabolic biodegradation was associated to the hydrogenotrophic methanogenesis (mainly Methanobacterium genus) in co-culture with fermentative bacteria (notably the genera Clostridium, Bacillus, Lactivibrio, Syntrophobacter and Syntrophorhabdus). The anaerobic fixed bed biofilm reactors proved to be highly efficient in biodegrading the antibiotics, preventing them from spreading to the environment.

Analyses of the Bacterial Contamination on Belgian Broiler Carcasses at Retail Level

Broilers are not equally exposed to bacterial contamination during rearing and processing, resulting in areas with different bacterial communities on carcasses at retail. The determination of these communities is also affected by the examination methods applied. The present study aimed to assess the bacterial communities on neck, breast, and back skin on broiler carcasses at retail through classical International Organization of Standardization based isolation methods combined with identification by matrix-assisted laser desorption ionization time-of-flight mass spectrum (MALDI-TOF MS) and 16S amplicon sequencing. Twelve commercially and eight organically reared broilers slaughtered in four slaughterhouses were examined. Significantly higher anaerobic bacterial counts were observed on the neck skin than on the breast and back skin. By the combination of cultivation and amplicon sequencing, remarkable shifts in bacterial communities were determined on the breast and back skin, but not on the neck skin. Although the aerobic bacteria contamination levels were not different between the areas, different bacterial communities were observed. The impact of the slaughterhouse to the overall microbial composition was rather small. Organically reared broilers had unique bacterial communities. In conclusion, compared to the breast skin, the neck, and back skin had a larger potential for bacterial spoilage, in particular when anaerobic storage conditions are applied. The distribution of bacteria on the different areas could be related to the contamination during slaughter as well as the bird-rearing methods.

Sulfate and metals removal from acid mine drainage in a horizontal anaerobic immobilized biomass (HAIB) reactor

The acid mine drainage (AMD) can causes negative impacts to the environment. Physico-chemical methods to treat AMD can have high operational costs. Through passive biological methods, such as anaerobic reactors, sulfate reduction, and recovery of metals are promoted. This study evaluated the performance of a horizontal anaerobic immobilized biomass (HAIB) reactor for the treatment of synthetic AMD using polyurethane foam as support material, and anaerobic sludge as inoculum. Ethanol was used as an electron donor for sulfate reduction, resulting in an influent chemical oxygen demand (COD) in the range of 500-1,500 mg/L and COD/sulfate ratio at 1. A gradual increase of sulfate and COD concentration was applied that resulted in COD removal efficiencies higher than 78%, and sulfate removal efficiencies of 80%. Higher sulfate and COD concentrations associated with higher hydraulic retention times (36 h) proved to be a better strategy for sulfate removal. The HAIB reactor was able to accommodate an increase in the SLR up to 2.25 g SO₄^2-/L d^-1 which achieved the greatest performance on the entire process. Moreover, the reactor proved a suitable alternative for reaching high levels of metal removal (86.95 for Zn, 98.79% for Fe, and 99.59% for Cu).

Effect of carbon-rich-waste addition as co-substrate on the performance and stability of anaerobic digestion of abattoir wastewater without agitation

Multiple wastes’ co-digestion is one of the alternatives for improved anaerobic digestion (AD) process of industrial and municipal wastes. The present work investigated the influence of fruit–vegetable solid waste (FVW) addition as a co-substrate on the performance of AD of abattoir wastewater (AWW). The co-digestion was done at a lab-scale-based experiment under mesophilic condition using a two-phase anaerobic sequencing batch reactor without agitation. It was tested at different mixing ratios (100%AWW; 75%AWW:25%FVW; 50%AWW:50%FVW; 25%AWW:75%FVW; 100%FVW) with the intention of looking for the best mixing ratio with the best performance. It was fed on a semi-continuous basis and operated for 18 days (d) total retention time (HRT): 3 days for the acidogenesis reactor and 15 days for methanogenesis reactor. The addition of FVW enhanced biogas yield and VS removal by 70.26% and 57.11%, respectively, at optimum mixing ratio. Moreover, to some extent improvement of AD process stability verified by the decreased TVFA:TAlk ratio and free ammonia nitrogen was observed upon progressive addition of FVW. Finally, this co-digestion process should further be studied for its performance at different HRTs with agitation.

Metagenomic insights into microbial characterizations in explaining the distinction of biofilter performance during start-up

As an effective alternative for dissolved nitrogen removal, biofilter closely associates its treatment performance to structural and/or operational conditions. In this study, a set of four different biofilters including MAVF (mature aerated vertical flow), NAVF (new aerated vertical flow), NVF (new non-aerated vertical flow), and BHF (baffled non-aerated horizontal flow) were employed to purify low C/N ratio (3.8) domestic wastewater. All the filters were packed with round ceramsite operated under varying hydraulic loading rates (HLRs) of 0.024-0.18 m/day. During the start-up, both the physicochemical and microbial characterizations were investigated. It was found that, carbon and nitrogen could achieve ideal removal in MAVF once added with further sedimentation, while phosphorus displayed an unsatisfactory sequestration in any of the four filters probably due to the high inflow load and/or lack of alternate anaerobic/aerobic conditions. Filter clustering based on percent removal and removal rate constant displayed a consistent pattern, which was similar to that based on taxa of phylum from 16S rRNA sequencing, or phylum/genus/species from shotgun metagenomic sequencing although there were obvious distinctions in taxa compositions among direct comparison. Meanwhile, gene function annotation revealed that filter clustering based on metabolic pathways was consistent with that based on purification performance. These consistencies might imply that the treatment performance was mainly determined by microbial degradation. The enrichment of specific functional microbes responsible for the degradation of certain pollutants, such as carbohydrates, matched well with the defined purification performance.

Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome

Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.

Biological wastewater treatment (anaerobic-aerobic) technologies for safe discharge of treated slaughterhouse and meat processing wastewater

Slaughterhouse industry generates considerable amount of wastewater rich in proteins, lipids, fibres, and carbohydrates. Numerous technologies such as electrocoagulation, membrane separation, advanced oxidation, physico-chemical processes, and biological treatment have been implemented for reducing the concentrations of these compounds. Nevertheless, this review aims to provide extensive information solely on the biological treatment (anaerobic and aerobic) of slaughterhouse wastewater. The advantages of anaerobic treatment are excellent organic matter removal, less sludge production, low energy requirement, execution of higher loading rates, and considerable production of biogas. Aerobic treatment on the other hand is a less sensitive process, possess lower start-up period, and efficient nutrient removal process. Numerous case studies are described to bestow maximum understanding of the wastewater characteristics, kind of treatment employed, and complications involved in managing and treating of slaughterhouse effluent. Additionally, role of microbial community involved in the treatment of slaughterhouse waste is also discussed. Sequential anaerobic and aerobic reactors are also reviewed in order to present their advantages over single bioreactors. Intermittent sequencing batch reactor is a promising technology than other high rate digesters in the removal of carbon, nitrogen, and phosphorous.

Characterizing phenol-removing consortia under methanogenic and sulfate-reducing conditions: potential metabolic pathways

Phenol removal was investigated in anaerobic fixed-structured bed reactors, namely R1 and R2, treating synthetic wastewater simulating the soluble fraction of vinasse under strictly methanogenic (R1) and simultaneous methanogenic/sulfidogenic conditions (R2). Next-generation sequencing (Illumina MiSeq System) was used to further characterize the microbial communities in both systems. Phenol was completely and stably removed in R1 after a short operating period (≈55 days). Conversely, phenol removal in R2 required a longer period for biomass acclimation (≈125 days) to reach levels equivalent to R1. Volatile fatty acids (VFA) accumulation in R2, mainly due to the inhibition of the acetoclastic methanogenesis by sulfide, may have limited phenol removal in the initial operating phases, as intermediate steps from phenol degradation are thermodynamically dependent on the removal of acetate, hydrogen and bicarbonate. Overall, the potential for anaerobically removing phenol from complex wastewaters was confirmed, even at low phenol/COD ratios. 16S rRNA gene sequencing analysis showed a high correlation of taxonomic profile between R1 and the inoculum, whereas a lower correlation was observed between R2 and the inoculum samples. Functional inference further indicated that Syntrophus and Bacillus genera in R1 and Clostridium genus in both reactors possibly played a key-role in phenol degradation.

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea)

Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of immune system. Wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea), migrating along the central Asian flyway, appear to be one of the most popular species in the rare birds rearing industries of China. However, the structure and function of the gut microbial communities associated with these two bird species remain poorly understood. Here, for the first time, we compared gut metagenomes from greylag geese to ruddy shelducks and investigated the similarities and differences between these two bird species in detail. Taxonomic classifications revealed the top three bacterial phyla, Firmicutes, Proteobacteria, and Fusobacteria, in both greylag geese and ruddy shelducks. Furthermore, between the two species, 12 bacterial genera were found to be more abundant in ruddy shelducks and 41 genera were significantly higher in greylag geese. A total of 613 genera (approximately 70%) were found to be present in both groups. Metabolic categories related to carbohydrate metabolism, metabolism of cofactors and vitamins, lipid metabolism, amino acid metabolism, and glycan biosynthesis and metabolism were significantly more abundant in ruddy shelducks, while greylag geese were enriched in nucleotide metabolism and energy metabolism. The herbivorous greylag geese gut microbiota harbored more carbohydrate‐active enzymes than omnivorous ruddy shelducks. In our study, a range of antibiotic resistance categories were also identified in the gut microbiota of greylag geese and ruddy shelducks. In addition to providing a better understanding of the composition and function of wild birds gut microbiome, this comparative study provides reference values of the artificial domestication of these birds.

Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing

The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset. The virome characterization revealed the presence of two viral families with Bacteria and Archaea as host, Myoviridae, and Siphoviridae. A wide functional diversity was found with predominance of genes involved in the metabolism of acetone, butanol, and ethanol synthesis; and one-carbon metabolism (e.g., methanogenesis). Genes related to the acetotrophic methanogenesis pathways were more abundant than methylotrophic and hydrogenotrophic, corroborating the taxonomic results that showed the prevalence of the acetotrophic genus Methanosaeta. Moreover, the dataset indicated a variety of metabolic genes involved in sulfur, nitrogen, iron, and phosphorus cycles, with many genera able to act in all cycles. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) revealed that microbial community contained 43 different types of antibiotic resistance genes, some of them were associated with growth chicken promotion (e.g., bacitracin, tetracycline, and polymyxin).