Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing

Up-flow anaerobic sludge blanket bioreactor for the production of carboxylates: effect of inocula on process performance and microbial communities

This research investigated the acidogenic fermentation (AF) of sugar cane molasses in an up-flow anaerobic sludge blanket (UASB) reactor for the production of carboxylates. The first step was to assess the optimum process temperature (25, 35 or 55 ºC) using two different granular inocula, one from a brewery company (BGS) and other from a paper plant company (PGS). These experiments determined that the most suitable temperature for carboxylates production was 25 ºC, obtaining higher bioconversions (27.3 ± 0.3% using PGS and 39.2 ± 0.2% using BGS), despite the low pH value recorded (4.0-4.2). Then, both inocula were tested in UASB reactors. As a consequence of the operational conditions (25 ºC, pH = 5.5-6, organic loading rate (OLR) = 3 gCOD·L-1·d-1 and hydraulic retention time (HRT) = 10 d), the microbial communities changed from those typical for biogas production to those specialised in the production of volatile fatty acids (VFAs). Indeed, the highest bioconversion efficiency (70.1%) was obtained with BGS, where uncultured Eubacteriaceae family microorganisms (56.0%) prevailed, enhancing the production of butyric acid (59.5 ± 2.4%w/w). Consequently, this inoculum was used to further identify the OLR threshold that should not be exceeded to attain optimal carboxylates production. OLR of 6 gCOD·L-1·d-1 resulted in a decrease in bioconversion efficiency (59.5%). The VFAs pool was dominated by butyric acid (63.0 ± 1.4%w/w at an OLR of 4.5 gCOD·L-1·d-1 and 52.8 ± 2.2%w/w at 6 gCOD·L-1·d-1). The microbial community became even more specialised, increasing the presence of Firmicutes and Actinobacteriota phyla, proving that the imposed conditions favoured the production of VFAs when operating semicontinuously fed UASB reactors.

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.

The effects of different pretreatment technologies on microbial community in anaerobic digestion process: A systematic review

Here we comprehensively review the available knowledge on effects of different pretreatment technologies on microbial population and microbial dynamics in anaerobic digestion (AD) fed with different substrates and different operational parameters. To identify peer-reviewed studies published in English-language journals, a comprehensive search was performed across multiple electronic databases. The eligible studies were analyzed to extract data and information pertaining to the configuration of anaerobic reactors, operational parameters, and various pretreatment processes such as chemical, biological, enzymatic, thermal, microaerobic, and ultrasonic. The findings derived from this current review demonstrated that different chemical, biological, and physical pretreatment technologies improve the biomethane potential (BMP) and potentially affect the dominant bacteria and archaea. Moreover, although hydrogenotrophic methanogenesis are more observed due to resistance to extreme conditions, methane production follows both aceticlastic and hydrogenotrophic pathways in AD assisted with different pretreatment process. Firmicutes and Bacteroidetes phyla of bacteria were the dominant hydrolytic bacteria due to synergetic effects of different pretreatment process on solubilization and bioavailability of recalcitrant substrates. In summary, a holistic understanding on bacteria and archaea communities, along with the mechanisms of the dominant microorganisms leads to enhanced stability and overall performance of anaerobic digestion (AD) processes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40201-024-00917-x.

Enhanced methane production from waste activated sludge by potassium ferrate combined with thermal hydrolysis pretreatment

Anaerobic digestion of waste activated sludge (WAS) was one of the directions of sludge treatment, but how to effectively improve the production of methane as a resource product of anaerobic digestion of sludge still needs further research. The study examined how the combination of potassium ferrate (PF) and thermal hydrolysis (TH) pretreatment affected methane production from sludge. The results demonstrated a positive synergistic effect on methane production with PF-TH pretreatment. Specifically, by employing a 0.05 g/g TSS (total suspended solids) PF in conjunction with TH at 80 °C for 30 min, the methane yield increased from 170.66 ± 0.92 to 232.73 ± 2.21 mL/g VSS (volatile suspended solids). The co-pretreatment of PF and TH has been substantiated by mechanism studies to effectively enhance the disintegration and biodegradability of sludge. Additionally, the variation of microbial community revealed an enrichment of active microorganisms associated with anaerobic digestion after treated with PF + TH, resulting in a total abundance increase from 11.87 to 20.45% in the PF + TH group.

Volatile fatty acid and methane production from vinasse and microalgae using two-stage anaerobic co-digestion

The effects of adding vinasse (VIN) as a co-substrate on the stability and production of volatile fatty acids (VFA) and methane (CH4) during the anaerobic digestion (AD) of microalgal biomass (MB) were evaluated. The AD system consisted of an acidogenic reactor (AR) followed by a methanogenic reactor (MR). The experiment was divided into phase I-start-up and AD of VIN; phase II-MB+VIN co-digestion (50:50 based on chemical oxygen demand (COD)); and phase III-co-digestion of pretreated MB and VIN (PTMB+VIN, 50:50). In phase I, the total amount of VFA in the AR increased from 240 to 2126 mg/L. In the MR, the conversion of VFA into CH4 yielded an average of 71 ± 37 NmL CH4/g CODin. In phase II, the initial CH4 production was 246 ± 31 mL CH4/g CODin but it decreased to 63 mL CH4/g CODin due to the accumulation of longer chain acids. More stable conditions were achieved after two hydraulic retention cycles and the average CH4 yield in this phase was 183 mL CH4/g CODin. In phase III, when using PTMB, 197 ± 72 NmL CH4/g CODin were obtained, i.e., a 2.7- and 1.1-fold increases compared to phases I and II, respectively. The predominance of acetate producers and syntrophic organisms suggests acetoclastic methanogenesis, confirmed by the occurrence of Methanosaeta (10.5%).

Anaerobic co-digestion of thermo-alkaline pretreated microalgae and sewage sludge: Methane potential and microbial community

To improve methane production from sewage sludge (SS), co-digestion of SS and microalgae (MA) was studied and the application of thermo-alkaline pretreatment to MA was evaluated. The results showed that thermo-alkaline pretreatment at 90°C for 120 min on MA was the optimum pretreatment condition. Furthermore, when the volatile solids (VS) ratio of SS and MA was 1:2, the methane yield reached maximum (368.94 mL/g VS). Fourier transform infrared (FT-IR) and thermogravimetric analysis confirmed the synergetic effects of thermo-alkaline pretreated MA on its co-digestion with SS. The analyses of microbial community indicated that Methanobacterium and Methanosarcina were the dominant methanogens during the co-digestion process. However, the relative abundance of Methanosarcina in thermo-alkaline pretreated groups was higher compared to unpretreated groups. The microbial community structure might be affected by thermo-alkaline pretreatment rather than by the MA dosage in the co-digestion.

Effects of enzymes on organic matter conversion in anaerobic fermentation of sludge to produce volatile fatty acids

Sludge hydrolysis is a vital step in anaerobic digestion of sludge. This study compared the efficacy of free versus immobilized enzymes at different concentrations in promoting sludge disintegration. Pretreatment with 1,000 mg/L immobilized enzymes was more efficient in promoting sludge disintegration than free enzymes at the same concentration. Under the optimized conditions, volatile fatty acids (VFAs) were produced at 10.6 g/L, accounting for 85 % of total soluble chemical oxygen demand. Improved VFA production was attributed to the release of large amounts of polysaccharides and proteins from the enzymatically pretreated sludge. Released organic matter are the substrates for VFAs generated by the determined microbial community of Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi. In this study, anaerobic fermentation was used to successfully convert organic matter in sludge into high-value-added VFAs. Therefore, this process can be selected as a strategy to reduce carbon emissions from wastewater treatment plants (WWTPs).

Effects of florfenicol on methane accumulation and changes in the structure of the prokaryotic community in a water-sediment system

Florfenicol has been widely used in the veterinary and aquaculture to control bacterial diseases because of its high efficacy, quick effect, and low cost. The water-sediment system has become an important sink for florfenicol, and the anaerobic environment of lake sediments is favorable for methane (CH₄) production. Although antibiotics may impact methanogenesis under anaerobic conditions, the influence of florfenicol on CH₄ accumulation in anaerobic water-sediment system remains uncertain. This study evaluated how florfenicol affects CH₄ accumulation and the structure of the prokaryotic community in a water-sediment system. Anaerobic systems with different florfenicol concentrations (0, 0.2, 1, 5 and 10 mg/L) were incubated and CH₄ accumulation, pH, total organic carbon content, degradation ratio of florfenicol, and structure of the prokaryotic community were monitored. It was found that CH₄ accumulation raised in low florfenicol (0.2 and 1 mg/L) systems during the growth period, while CH₄ accumulation declined in high florfenicol (5 and 10 mg/L) systems. In the first 13 d, 83.67-99.30 % of florfenicol degraded in different treatments. The addition of florfenicol also influenced the structure of the prokaryotic community of the sediments. Proteobacteria and Chloroflexi were dominant at the phylum level. The dominant taxa at the order level gradually changed from Methanomicrobiales to Methanobacteriales, and finally to Methanosarcinales, indicating the dynamic transformation of methanogens in the reactor. This study reveals the effects of florfenicol on CH₄ production under anaerobic conditions and provides a theoretical basis for further research on the underlying mechanisms. The findings also provide some basic data on the impact of new pollutants on the global carbon cycle and greenhouse gas emission.

Stability of the Anaerobic Digestion Process during Switch from Parallel to Serial Operation—A Microbiome Study

Anaerobic digestion is a common procedure of treating sewage sludge at wastewater treatment plants. However, plants differ in terms of the number of reactors and, in case of several reactors, their operation mode. To confirm the flexibility of well adapted, full-scale anaerobic digestion plants, we monitored the physicochemical process conditions of two continuously stirred tank reactors over one hydraulic retention time before and after the operation mode was switched from parallel to serial operation. To investigate changes in the involved microbiota, we applied Illumina amplicon sequencing. The rapid change between operation modes did not affect the process performance. In both parallel and serial operation mode, we detected a highly diverse microbial community, in which Bacteroidetes, Firmicutes, Proteobacteria and Claocimonetes were high in relative abundance. While a prominent core microbiome was maintained in both configurations, changes in the involved microbiota were evident at a lower taxonomical level comparing both reactors and operation modes. The most prominent methanogenic Euryarchaeota detected were Methanosaeta and cand. Methanofastidiosum. Volatile fatty acids were degraded immediately in both reactors, suggesting that the second reactor could be used to produce methane on demand, by inserting easily degradable substrates.

Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products

Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.

Light stimulation strategy for promoting bio-hydrogen production: Microbial community, metabolic pathway and long-term application

Light stimulation strategy for promoting bio-H₂ production was firstly investigated with incandescent light. The light condition controlled by photon number (N_R, 0.63 × 10⁴-6.25 × 10⁴ μmol/(day∙L)) was applied to stimulate H₂ fermentation process. The optimal N_R of 3.75 × 10⁴ μmol/(day∙L) contributed to 1.4 folds H₂ yield of the dark reactor and promoted efficient H₂ producing pathway (acetate and nicotinamide adenine dinucleotide pathway) with increased microbial activities. Furthermore, the effect of light stimulation on microbial community was identified. Fervidobacterium, Coprothermobacter and OPB95 were the dominant genera that could be activated by light stimulation for promoting acetate pathway and contribute to higher H₂ production. Moreover, long-term operation showed more stable and higher H₂ production of light stimulated bioreactor than the dark one, which resulted from the light stimulated metabolic pathway, increased sludge conductance and promoted microbial immobilization. This novel light stimulation strategy is promising for future application on promoting bio-H₂ production.

Sludge disintegration and anaerobic digestion enhancement by alkaline-thermal pretreatment: Economic evaluation and microbial population analysis

Alkaline-thermal pretreatment was examined for waste activated sludge (WAS) disintegration and subsequent anaerobic digestion (AD). Pretreatment at 60 °C was estimated to provide better economic benefits than higher temperature conditions. The maximum methane yield of 215.6 mL/g COD was achieved when WAS was pretreated at 60 °C and pH 10 for 24 h, which was 46.6% higher than untreated WAS. The pretreatment condition also provided the maximum net savings. The degree of sludge disintegration, considering both loosely bound-extracellular polymeric substance and soluble COD, would be a better indicator to predict anaerobic digestibility than the solubilization rate that considers soluble COD alone. Microbial analysis implied that pretreatment facilitated the growth of hydrolytic bacteria, phyla Bacteroidetes and Firmicutes. In addition, sludge pretreatment enhanced the growth of both acetoclastic and hydrogenotrophic methanogens, genera Methanosaeta and Methanobacterium. The mild AT-PT would be useful to enhance the digestion performance and economic benefit of WAS digestion.

Effect of Sodium on Methanogens in a Two-Stage Anaerobic System

This study evaluated the effects of sodium on anaerobic biomass from the second-stage reactor of a two-stage anaerobic digester. The results indicated that methanogens showed a relatively high sodium tolerance of 2.4 g Na+ L−1. Microbial community analysis showed that viable Methanomicrobiales was the most abundant population by a combined propidium monoazide cross-linking quantitative polymerase chain reaction technique. There was a population shift towards higher abundance of Thermotoga (0.02%), Clostridium (2.50%) and Methanoculleus (13.80%). Biomass activity in relation to increased sodium concentrations was investigated with the adenosine triphosphate test coupled with extracellular polymeric substances measurement. The results showed biomass activity decreased from 33 to 16 µg g−1 volatile suspended solids as sodium concentrations increased from 1.3 to 9.1 g Na+ L−1. Higher EPS production, particularly a greater predominance of carbohydrates, was stimulated by higher sodium concentrations. This study provides insights into the superiority of sodium tolerance of two-stage anaerobic digester in compared with a single-stage anaerobic system.

Microbial consortia adaptation to substrate changes in anaerobic digestion

Renewable natural gas (RNG) produced from anaerobic digestion (AD) of agricultural residues is emerging a serious biofuel alternative. Complex nature of lignocellulosic biomass residues coupled with complex biochemical transformations involving a large spectrum of microbial communities make anaerobic digestion of biomass difficult to understand and control. The present work aims at studying adaptation of microbial consortia in AD to substrates changes and correlating these to biogas generation. The double edged study deals with (a) using a common starting culture inoculum on different fractions of pretreated lignocellulosic biomass (LBM) fractions; and (b) using different starter inocula for gas generation from simple glucose substrate. Taxonomic analysis using 16S amplicon sequencing is shown to highlight changes in microbial community structure and predominance, majorly in hydrolytic bacterial populations. Observed variations in the rate of digestion with different starter inocula could be related to differences in microbial community structure and relative abundance. Results with different treated biomass fractions as substrates indicated that AD performance could be related to abundance of substrate-specific microbial communities. The work is a step to a deeper understanding of AD processes that may lead to better control and operation of AD for super-scale production of RNG from biomass feedstocks.

Syngas biomethanation: effect of biomass-gas ratio, syngas composition and pH buffer

The concept of syngas biomethanation is attractive, however, it still needs improvement in optimizing the operational conditions. In the present study, syngas fermentations under different carbon monoxide (CO), carbon dioxide (CO₂) and hydrogen (H₂) compositions were conducted under two different biomass-gas ratio (BGR) systems. The results showed that high BGR enhanced the CO consumption rate, achieving a 60% enhancement with CO as the sole substrate. Stoichiometric H₂ addition could successfully convert all the CO and CO₂ to pure methane, however, higher H₂ partial pressure might decline the CO consumption due to pH inhibition from consumption of bicarbonate. Microbial analysis showed different syngas composition could affect the bacteria community, while, archaea community was only slightly affected with Methanothermobacter as the dominant methanogen. This study provided strategy for efficient syngas biomethanation and deeper insight into effect of H₂ addition on CO conversion under different BGR systems.

Enhanced methane production from waste activated sludge by potassium ferrate combined with ultrasound pretreatment

This study explored the effect of potassium ferrate (PF) combined with ultrasound (US) pretreatment on methane generation from sludge by a series of experiments and simulations. Batch experiments showed that the pretreatment of PF coupled with US exhibited positively synergy on the methane yield. And by the pretreatment of 0.05 g/g TSS (total suspended solids) PF cooperated with US (1 W/mL, 25 kHz, 15 min), the methane yield was enhanced from 180.62 ± 3.26 to 228.83 ± 4.76 mL/g VSS (volatile suspended solids). Mechanism studies confirmed that the co-pretreatment of PF and US efficiently promoted sludge disintegration, and the biodegradability of sludge organics was obviously enhanced. Microbial community analysis showed that the functional microorganisms participating in sludge anaerobic digestion were enriched by PF cooperated with US pretreatment, with the total abundance enhanced from 12.96% in the control to 17.96% in PF + US pretreated reactor.

In-situ biogas upgrading by bio-methanation with an innovative membrane bioreactor combining sludge filtration and H2 injection

A bioreactor using membrane technologies was used to demonstrate the feasibility of in-situ bio-methanation coupled to industrial wastewater treatment for biogas upgrading. High biogas productivity (1.7 Nm³_Biogas/m³_Bioreactor/day) with high CH₄ content (97.9%) was reached. In-situ bio-methanation did not affect the COD removal efficiency of anerobic digestion (>94%). Process resilience has been tested for both substrate overload and H₂ intermittence injection. Recovery of high CH₄ content after 7 days without H₂ injection occurred within few hours. Influence of microbial community has been studied showing that both hydrogenotrophic and homoacetogenic-acetoclastic pathways were involved.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

Response of Microbial Community to Induced Failure of Anaerobic Digesters Through Overloading With Propionic Acid Followed by Process Recovery

In order to effectively use microbial-based strategies to manage anaerobic digesters, it is necessary to distinguish between community shifts that are part of the natural dynamic of the system and shifts caused by environmental or operational disturbances. The objective of this research study was to evaluate the significance of changes in the microbial community of anaerobic digesters during failure in correlation to operational parameters such as an organic acid overload. Five continuously stirred 0.5 L reactors were set-up as semi-continuously-fed, mesophilic dairy manure digesters with a 30-day hydraulic retention time. After a 120-day stabilization period, two digesters were kept as controls, while the organic loading rates in the triplicate set were increased step-wise to ultimately provide a shock-load leading to failure using propionic acid spikes. Acidosis resulting in near cessation of biogas and termination of methane production occurred between 4 and 7 weeks, after which all the digesters continued to be fed only dairy manure. The shock loading of propionic acid led to an accumulation of mainly acetate and propionate, with low levels of iso-butyrate, butyrate, iso-valerate, and valerate. High-throughput Illumina sequencing of the V4 region of the bacterial and archaeal 16S rRNA gene in digester samples showed a significant change in the microbial community composition during propionic acid overload, followed by a return to the original composition with regular feedstock. Bacterial genera whose relative abundance decreased during the inhibition stage included Sedimentibacter, Syntrophomonas, TSCOR003.O20, and Marinilabiaceae, while the relative abundance of Lachnospiraceae, Ruminococcus, Mogibacteriaceae, Pyramidobacter, and Bacteroides increased. The relative abundance of dominant methanogens, Methanosarcina and Methanobacterium, although initially resistant, were decreased (from 91.71 to 12.14% and from 2.98 to 0.73%, respectively) during inhibition, while Methanobrevibacter and Methanosphaera that were prominent in the manure feedstock increased from 17.36 to 79.45% and from 0.14 to 1.12%, respectively. Shifts in bacterial and archaeal compositions, back to their pre-shock steady state after failure, highlight the digester's microbial resilience and recovery potential.

A metagenomic assessment of microbial communities in anaerobic bioreactors and sediments: Taxonomic and functional relationships

The present study used metagenomic sequencing, metagenome assembly and physical-chemical analysis to describe taxonomically and functionally 3 anaerobic bioreactors treating manure (LI), brewery (BR) and cornmeal (CO) wastes, and an anaerobic estuarine sediment (ES). Proteobacteria, Firmicutes, Euryarchaeota and Bacteroidetes were the most abundant Phyla in all metagenomes. A bacteria/archaea ratio of 3.4 was found in the industrial full-scale anaerobic bioreactors BR and CO, while ratios greater than 10 were found for LI and ES. Canonical correspondence analysis showed that environmental variables such as chemical oxygen demand, lipid content, and ammonium nitrogen influenced the ordination of taxonomic groups. Mesotoga prima was linked to high-temperature conditions, particularly in the BR bioreactor, along with the presence of heat shock proteins genes. Likewise, the hydrogenotrophic methanogen, Methanoregula formicica, was associated with high ammonium concentration in LI bioreactor. The interactions of microbes with specific methanogenic pathways were identified using Clusters of Orthologous Groups (COG) functions, while metagenome-assembled genomes (MAGs) further confirmed relationships between taxa and functions. Our results provide valuable information to understand microbial processes in anaerobic environments.

Carbon monoxide conversion and syngas biomethanation mediated by different microbial consortia

Syngas biomethanation is an attractive process for extending application of gasification products. In the present study, anaerobic sludges from three methanogenic reactors feeding cattle manure (CS), sewage sludge (SS) and gaseous H₂/CO₂ (GS) were used to investigate the effect of microbial consortia composition on syngas biomethanation. The results showed that CS presented the highest CO consumption rate due to its highest relative abundance of CO consuming bacteria. The CO was mainly converted to acetate, and syntrophic acetate oxidization (SAO) bacteria converted acetate to H₂/CO₂ for hydrogenotrophic methanogenesis in CS and SS. However, acetate was accumulated in GS for lacking acetoclastic methanogens and SAO bacteria, leading to lower biomethanation efficiency. Additionally, adding stoichiometric H₂ could convert CO and CO₂ to nearly pure methane, while, the CO consumption rate declined in H₂ added systems. The results present novel insights into microbial consortia on CO conversion and syngas biomethanation.

Effects of different hypochlorite types on the waste activated sludge fermentation from the perspectives of volatile fatty acids production, microbial community and activity, and characteristics of fermented sludge

The effects of different hypochlorite types (namely Ca(OCl)₂ and NaOCl) on the waste activated sludge (WAS) anaerobic fermentation, and microbial community and activity were investigated. The results indicated that both Ca(OCl)₂ and NaOCl contributed to volatile fatty acids (VFAs) production by simultaneously enhancing the solubilization, hydrolysis and acidification processes. The maximal VFAs was respectively 1379.5 (at 10 d) and 1621.5 (at 8 d) mg COD/L at the optimal dose of NaOCl and Ca(OCl)₂ while it was merely 157.4 (at 6 d) mg COD/L in the control. However, the Ca(OCl)₂ might affect the anaerobic process in a continuous mode while the NaOCl was relatively transient, which caused distinctive influences on the microbial structure and activity, and subsequently VFAs production in WAS fermentation systems. Moreover, Ca(OCl)₂ treatments showed advantages over NaOCl on WAS dewatering and VSS reduction, implying the superiority of utilizing Ca(OCl)₂ as additives for WAS disposal.

Comparative Analysis of Sample Extraction and Library Construction for Shotgun Metagenomics

Human fecal specimens, serve as important materials, are widely used in the field of microbiome research, in which inconsistent results have been a pressing issue. The possible attribute factors have been proposed including the specimen status after preservation, extracted DNA quality, library preparation protocol, and sample DNA input. In this study, quality comparisons for shotgun metagenomics sequencing were performed between 2 DNA extraction methods for fresh and freeze-thaw samples, 2 library preparation protocols, and various sample inputs. The results indicate that Mag-Bind® Universal Metagenomics Kit (OM) outperformed DNeasy PowerSoil Kit (QP) with a higher DNA quantity. Controlling on library preparation protocol, OM detected on-average more genes than QP. For library construction comparison by controlling on the same DNA sample, KAPA Hyper Prep Kit (KH) outperformed the TruePrep DNA Library Prep Kit V2 (TP) with the higher number of detected genes number and Shannon index. No significant differences were found in taxonomy between 2 library preparation protocols using the fresh, freeze-thaw and mock community samples. No significant difference was observed between 250 and 50 ng DNA inputs for library preparation on both fresh and freeze-thaw samples. Through the preliminary study, a combined protocol is recommended for performing metagenomics studies, by using OM method plus KH protocol as well as suitable DNA quantity on either fresh or freeze-thaw samples. Our findings provide clues for potential variations from various DNA extraction methods, library protocols, and sample DNA inputs, which are critical for consistent and comprehensive profiling of the human gut microbiome.

Enhanced volatile fatty acids production from waste activated sludge with synchronous phosphorus fixation and pathogens inactivation by calcium hypochlorite stimulation

An efficient approach for synchronous volatile fatty acids (VFAs) promotion, phosphorus fixation and pathogens inactivation during waste activated sludge (WAS) anaerobic fermentation was achieved with optimal calcium hypochlorite (Ca(ClO)₂) stimulation. The maximal VFAs were 3.6 folds of control in reactors with 0.01 g Ca(ClO)₂/g TSS addition. The low dosage of Ca(ClO)₂ enhanced WAS solubilization and hydrolysis by disrupting the extracellular polymeric substance (EPS) effectively. Sufficient substrates for fermentative bacteria were thereby provided with the maintenance of acceptable microbial activity and viability. However, high dosage of Ca(ClO)₂ deteriorated the performance of anaerobic fermentation due to its strong oxidative ability, resulting in cell lysis greatly. Moreover, the largely released phosphorus during WAS fermentation was effectively precipitated and removed by the combination of Ca²⁺ at 0.01 g Ca(ClO)₂/g TSS dosage. In addition, Ca(ClO)₂ had distinguished effects on pathogens inactivation. The simultaneous phosphorus fixation and pathogens reduction during VFAs production increased the utilization value of fermentation liquid and benefitted the further disposal of fermented sludge.

Efficient nitrous oxide recovery from incineration leachate by a nosZ-deficient strain of Pseudomonas aeruginosa

In this study, nitrous oxide was recovered from a lab-scale moving-bed biofilm reactor (MBBR) treating partial nitrification-treated leachate supplemented with a nosZ-deficient strain of Pseudomonas aeruginosa. Batch culture tests with the nosZ-deficient strain determined that the threshold for free nitrous acid (FNA) inhibition was 0.016 mg/L and that FNA concentrations above this threshold severely inhibited denitrification and transcription of genes from the dissimilatory nitrate reduction pathway (narG, nirS, and norB). High nitrite removal and N₂O conversion efficiencies (>95%) were achieved with long-term operation of this MBBR. N₂O accounted for the majority of biogas (80%) produced when the MBBR was fed partial nitrification-treated leachate with high nitrite concentrations and the drainage ratio was adjusted to 30%. Bacterial community analysis revealed that the nosZ-deficient Pseudomonas strain remained metabolically active and was primarily responsible for denitrification processes in the reactor. This study presents a promising method for N₂O recovery from incineration leachate.

Microalgae Biomass as a Potential Feedstock for the Carboxylate Platform

Volatile fatty acids (VFAs) are chemical building blocks for industries, and are mainly produced via the petrochemical pathway. However, the anaerobic fermentation (AF) process gives a potential alternative to produce these organic acids using renewable resources. For this purpose, waste streams, such as microalgae biomass, might constitute a cost-effective feedstock to obtain VFAs. The present review is intended to summarize the inherent potential of microalgae biomass for VFA production. Different strategies, such as the use of pretreatments to the inoculum and the manipulation of operational conditions (pH, temperature, organic loading rate or hydraulic retention time) to promote VFA production from different microalgae strains, are discussed. Microbial structure analysis using microalgae biomass as a substrate is pointed out in order to further comprehend the roles of bacteria and archaea in the AF process. Finally, VFA applications in different industry fields are reviewed.

Response of the microbial community to the methanogenic performance of biologically hydrolyzed sewage sludge with variable hydraulic retention times

Hyperthermophilic biological hydrolysis of sewage sludge was applied before long-term anaerobic digestion to investigate how shortening hydraulic retention times (HRT, 20-5d) affected methanogenic performances and microbial dynamics. Results indicated that although the three different HRTs provided a stable process with a steady-state of methane production, both methane yield (161 L kg-VS_in^-1_, 25% higher) and volatile solids removal (VS, 50%, 2-fold higher) increased during longer HRTs. Redundancy analysis results indicated that Sporosarcina and Methnosarcina positively correlated to VS removal and methane yield, and negatively correlated to volatile fatty acids (VFAs) accumulation. The relative abundance of Coprothermobacter (>60%), syntrophic acetate oxidation bacteria (SAOB), and Methanospirillum (8-15%), increased during shorter HRTs. A slight shift to two-stage acetate conversion was observed during shorter HRTs. The results demonstrated that HRTs played a key role in shaping microbial structure, leading to a new steady-state of microbial community profiles and process performances at variable HRTs.

High variations of methanogenic microorganisms drive full-scale anaerobic digestion process

Anaerobic digestion is one of the most successful waste management strategies worldwide, wherein microorganisms play an essential role in reducing organic pollutants and producing renewable energy. However, variations of microbial community in full-scale anaerobic digesters, particularly functional groups relevant to biogas production, remain elusive. Here, we examined microbial community in a year-long monthly time series of 3 full-scale anaerobic digesters. We observed substantial diversification in community composition, with only a few abundant OTUs (e.g. Clostridiales, Anaerolineaceae and Methanosaeta) persistently present across different samples. Similarly, there were high variations in relative abundance of methanogenic archaea and methanogenic genes, which were positively correlated (r² = 0.530, P < 0.001). Variations of methanogens explained 55.7% of biogas producing rates, much higher than the explanatory percentage of environmental parameters (16.4%). Hydrogenotrophic methanogens, especially abundant Methanomicrobiales taxa, were correlated with biogas production performance (r = 0.665, P < 0.001) and nearly all methanogenic genes (0.430 < r < 0.735, P < 0.012). Given that methanogenic archaea or genes are well established for methanogenesis, we conclude that high variations in methanogenic traits (e.g. taxa or genes) are responsible for biogas production variations in full-scale anaerobic digesters.

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater

To investigate the effects of temporal variations of process parameters on microbial community structures in the two types of full-scale anaerobic digester treating swine wastewater, three full-scale anaerobic digesters were monitored. An anaerobic filter (AF)-type digester located in Gong-Ju (GJ) showed the highest COD removal among three digesters and maintained stable efficiency. A digester in Hong-Seong (HS) was of the same type as it GJ and showed improved efficiency over the sampling period. A continuously stirred tank reactor (CSTR)-type digester in Soon-Cheon (SC) showed decreasing efficiency due to a high residual concentration of VFAs and NH₄⁺. These process efficiencies were closely correlated to the Simpson indices of the methanogenic communities. Genera Bacillus, Methanosaeta, and Methanospirillum that have filamentous morphology were dominant in both AF-type digesters, but genera Acholeplasma, Methanosarcina, and Methanoculleus that have spherical or coccoid morphology were dominantly abundant in the CSTR-type digester. Correlation between populations suggests a possible syntrophic relationship between genera Desulfobulbus and Methanosaeta in digesters GJ and HS.

Effects of Copper Oxide Nanoparticles on Paddy Soil Properties and Components

The wide use of metal-based nanoparticles (MNPs) will inevitably lead to their release into soil, and consequently affect the quality and ecological functions of soil environments. In this study, two paddy soils with different properties were exposed to CuO NPs to evaluate the transformation of CuO NPs and their effects on soil properties and components. The results of single chemical extraction and X-ray absorption fine structure analysis showed that CuO NPs could release Cu ions once being applied into the flooding paddy soil and then progress toward the more stable forms (Cu₂S and Cu(OH)₂). CuO NPs could change the soil properties by increasing the pH and Eh of the lower organic matter-soil rather than those of the higher organic matter-soil. Furthermore, we found that the 1000 mg/kg CuO NPs could accelerate the degradation or mineralization of the organic matter, as well as the Fe reduction process, by increasing the Fe(II) content by 293% after flooding for 60 days in the lower organic matter soil. The microbial biomass in both soils was severely inhibited by CuO NPs and the organic matter could partly mitigate the negative effects of CuO NPs.

Effects of CO on hydrogenotrophic methanogenesis under thermophilic and extreme-thermophilic conditions: Microbial community and biomethanation pathways

Coke oven gas is considered as a potential hydrogen source for biogas bio-upgrading. In this study, the effects of CO on biomethanation performance and microbial community structure of hydrogenotrophic mixed cultures were investigated under thermophilic (55 °C) and extreme-thermophilic (70 °C) conditions. 5% (v/v) CO did not inhibit hydrogenotrophic methanogenesis during semi-continuous operation, and 83-97% CO conversion to CH₄ was achieved. Methanothermobacter thermoautotrophicus was the dominant methanogen at both temperatures and was the main functional archaea associated with CO biomethanation. Specific methanogenic activity test results showed that long-term 5% CO acclimation shortened the lag phase from 5 h to 1 h at 55 °C and 15 h to 3 h at 70 °C. CO₂ was the preferred carbon source over CO for hydrogenotrophic methanogens and CO consumption only started when CO₂ was completely depleted. M. thermoautotrophicus dominated mixed cultures showed a great potential in simultaneous hydrogenotrophic methanogenesis and CO biomethanation.

Genetic repertoires of anaerobic microbiomes driving generation of biogas

BACKGROUND

Biogas production is an attractive technology for a sustainable generation of renewable energy. Although the microbial community is fundamental for such production, the process control is still limited to technological and chemical parameters. Currently, most of the efforts on microbial management system (MiMaS) are focused on process-specific marker species and community dynamics, but a practical implementation is in its infancy. The high number of unknown and uncharacterized microorganisms in general is one of the reasons hindering further advancements.

RESULTS

A Biogas Metagenomics Hybrid Assembly (BioMETHA) database, derived from microbiomes of biogas plants, was generated using a dedicated assembly strategy for different metagenomic datasets. Long reads from nanopore sequencing (MinION) were combined with short, more accurate second-generation sequencing reads (Illumina). The hybrid assembly resulted in 231 genomic bins each representing a taxonomic unit with an average completeness of 47%. Functional annotation identified 13,190 non-redundant genes covering roughly 207 k coding sequences. Mapping rates of metagenomics DNA derived from diverse biogas plants and laboratory reactors increased up to 73%. In addition, an EC (enzyme commission) reference sequence collection (ERSC) was generated whose genes are crucial for biogas-related processes, consisting of 235 unique EC numbers organized in 52 metabolic modules. Mapping rates of metatranscriptomic data to this ERSC revealed coverages of up to 93%. Process parameters and imbalances of laboratory reactors could be reconstructed by evaluating abundance of biogas-specific metabolic modules using metatranscriptomic data derived from various fermenter systems.

CONCLUSION

This newly established metagenomic hybrid assembly in combination with an EC reference sequence collection might help to shed light on the microbial dark matter of biogas plants by contributing to the development of a reference for biogas plant microbiome-specific gene sequences. Considering a biogas microbiome as a complex meta-organism expressing a meta-transcriptome, the approach established here could lay the foundation for a function-based microbial management system.

The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels

Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated.

Changes in microbial communities during volatile fatty acid production from cyanobacterial biomass harvested from a cyanobacterial bloom in a river

Volatile fatty acid (VFA) production, utilization of soluble organic compounds, and associated microbial consortia were investigated after different pretreatments (untreated, alkaline, and thermal-alkaline) using cyanobacterial biomass as a substrate. Compared to the untreated control, soluble carbohydrate concentrations were almost the same after alkaline and thermal-alkaline pretreatments, but soluble protein concentration was 1.58 times higher after alkaline pretreatment and 1.81 times higher after thermal-alkaline pretreatment. However, the highest degree of acidification was obtained after alkaline pretreatment (55.36 ± 3.00%). Microbial communities in the untreated control differed only slightly from those after thermal-alkaline pretreatment, but were clearly distinct from those after alkaline pretreatment. After alkaline pretreatment, protein-utilizing bacteria became relatively predominant. These results revealed the relationships between efficiency of VFA production and the shift in microbial community.

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions

Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Flexible metagenome analysis using the MGX framework

BACKGROUND

The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.

RESULTS

We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.

CONCLUSIONS

With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.

Redundancy in Anaerobic Digestion Microbiomes during Disturbances by the Antibiotic Monensin

The antibiotic monensin is fed to dairy cows to increase milk production efficiency. A fraction of this monensin is excreted into the cow manure. Previous studies have found that cow manure containing monensin can negatively impact the performance of anaerobic digesters, especially upon first introduction. Few studies have examined whether the anaerobic digester microbiome can adapt to monensin during the operating time. Here, we conducted a long-term time series study of four lab-scale anaerobic digesters fed with cow manure. We examined changes in both the microbiome composition and function of the anaerobic digesters when subjected to the dairy antibiotic monensin. In our digesters, monensin was not rapidly degraded under anaerobic conditions. The two anaerobic digesters that were subjected to manure from monensin feed-dosed cows exhibited relatively small changes in microbiome composition and function due to relatively low monensin concentrations. At higher concentrations of monensin, which we dosed directly to control manure (from dairy cows without monensin), we observed major changes in the microbiome composition and function of two anaerobic digesters. A rapid introduction of monensin to one of these anaerobic digesters led to the impairment of methane production. Conversely, more gradual additions of the same concentrations of monensin to the other anaerobic digester led to the adaptation of the anaerobic digester microbiomes to the relatively high monensin concentrations. A member of the candidate OP11 (Microgenomates) phylum arose in this anaerobic digester and appeared to be redundant with certain Bacteroidetes phylum members, which previously were dominating.IMPORTANCE Monensin is a common antibiotic given to dairy cows in the United States and is partly excreted with dairy manure. An improved understanding of how monensin affects the anaerobic digester microbiome composition and function is important to prevent process failure for farm-based anaerobic digesters. This time series study demonstrates how anaerobic digester microbiomes are inert to low monensin concentrations and can adapt to relatively high monensin concentrations by redundancy in an already existing population. Therefore, our work provides further insight into the importance of microbiome redundancy in maintaining the stability of anaerobic digesters.

Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses

Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM) for hydrogen and methane production from waste-activated sludge (WAS) was investigated. The TM process was also compared to a process with mesophilic alkaline fermentation followed by a mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The results showed that both hydrogen yield (74.5 ml H₂/g volatile solids [VS]) and methane yield (150.7 ml CH₄/g VS) in the TM process were higher than those (6.7 ml H₂/g VS and 127.8 ml CH₄/g VS, respectively) in the MM process. The lowest methane yield (101.2 ml CH₄/g VS) was obtained with the M process. Taxonomic results obtained from metagenomic analysis showed that different microbial community compositions were established in the hydrogen reactors of the TM and MM processes, which also significantly changed the microbial community compositions in the following methane reactors compared to that with the M process. The dynamics of bacterial pathogens were also evaluated. For the TM process, the reduced diversity and total abundance of bacterial pathogens in WAS were observed in the hydrogen reactor and were further reduced in the methane reactor, as revealed by metagenomic analysis. The results also showed not all bacterial pathogens were reduced in the reactors. For example, Collinsella aerofaciens was enriched in the hydrogen reactor, which was also confirmed by quantitative PCR (qPCR) analysis. The study further showed that qPCR was more sensitive for detecting bacterial pathogens than metagenomic analysis. Although there were some differences in the relative abundances of bacterial pathogens calculated by metagenomic and qPCR approaches, both approaches demonstrated that the TM process was more efficient for the removal of bacterial pathogens than the MM and M processes.IMPORTANCE This study developed an efficient process for bioenergy (H₂ and CH₄) production from WAS and elucidates the dynamics of bacterial pathogens in the process, which is important for the utilization and safe application of WAS. The study also made an attempt to combine metagenomic and qPCR analyses to reveal the dynamics of bacterial pathogens in anaerobic processes, which could overcome the limitations of each method and provide new insights regarding bacterial pathogens in environmental samples.

Proteiniborus indolifex sp. nov., isolated from a thermophilic industrial-scale biogas plant

A novel strictly anaerobic bacterium, designated strain BA2-13^T, was isolated from a thermophilic industrial-scale biogas plant. Cells were rod-shaped and Gram-stain-positive. Growth occurred at temperatures of 25 to 50 °C and between pH 6.3 and 9.5. Strain BA2-13^T produced indole. Cell growth was stimulated by yeast extract, peptone, meat extract, a mixture of 20 amino acids, glucose, pyruvate and ribose. When grown on peptone and yeast extract, the main fermentation products were acetic acid, H₂ and CO₂. The predominant cellular fatty acids were iso-C_15 : 0 and iso-C_14 : 0 3-OH. Major polar lipids were diphosphatidylglycerol, glycolipids, phospholipids and phosphatidylgycerol. Phylogenetic analysis based on 16S rRNA gene nucleotide sequence analysis placed strain BA2-13^T within the order Clostridiales showing closest affiliation with Proteiniborusethanoligenes with 95.9 % sequence identity. Physiological, genotypic and chemotaxonomic differences of strain BA2-13^T from P. ethanoligenes support the description of a new species within the genus Proteiniborus for which we suggest the name Proteiniborusindolifex sp. nov. (type strain BA2-13^T=DSM 103060^T=LMG 29818^T).

Do microbial communities in an anaerobic bioreactor change with continuous feeding sludge into a full-scale anaerobic digestion system?

Microbial communities of sludge samples from a full-scale anaerobic digestion (AD) fed with primary sludge (PS) and excess sludge (ES) were analyzed using qPCR and MiSeq. The results showed that the microbial composition of digested sludge remained relatively stable but was partially changed by microbial immigration from feeding sludge. The dominant archaea in the digested sludge were largely the same as those in the feeding sludge, but their abundances differed markedly. The dominant fungal genera in the digested sludge were different from those in PS but were similar to those in ES. Various differences in bacterial community differences between digested sludge and PS/ES were observed. Notably, this study is the first to suggest Verrucomicrobia is the predominant bacterial phylum in the digested sludge, and that numerous unreported microorganisms belonging to the order LD1-PB3 existed in this AD system and potentially played roles in the processes of hydrolysis, fermentation, and acetogenesis.

A New Combination of Substrates: Biogas Production and Diversity of the Methanogenic Microorganisms

Agriculture, food industry, and manufacturing are just some of the areas where anaerobic technology can be used. Currently, anaerobic technologies are mainly used for wastewater treatment, solid waste treatment, or for the production of electrical and thermal energy from energy crops processing. However, a clear trend is towards more intensive use of this technology in biomass and biodegradable waste processing and hydrogen or biomethane production. An enormous number of anaerobic digesters are operating worldwide but there is very little information about the effect of different substrate combinations on the methanogens community. This is due to the fact that each of the anaerobic digesters has its own unique microbial community. For the most effective management of anaerobic processes it would be important to know the composition of a consortium of anaerobic microorganisms present in anaerobic digesters processing different input combinations of raw material. This paper characterizes the effect of the input raw materials on the diversity of the methanogen community. Two predominant microorganisms in anaerobic digesters were found to be 99% identity by the sequences of the 16S rRNA gene to the Methanoculleus and Thermogymnomonas genera deposited in GenBank.

Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics

BACKGROUND

Part-stream low-frequency ultrasound (LFUS) was one of the common practices for sludge disintegration in full-scale anaerobic digestion (AD) facilities. However, the effectiveness of part-stream LFUS treatment and its effect on AD microbiome have not been fully elucidated.

METHODS

Here we testified the effectiveness of part-stream LFUS pretreatment by treating only a fraction of feed sludge (23% and 33% total solid of the feed sludge) with 20 Hz LFUS for 70 s. State-of-the-art metagenomic and metatranscriptomic analysis was used to investigate the microbial process underpinning the enhanced AD performance by part-stream LFUS pretreatment.

RESULTS

By pretreating 33% total solid of the feed sludge, methane yield was increased by 36.5%, while the volatile solid reduction ratio remained unchanged. RNA-seq of the microbiome at stable stage showed that the continuous dosage of easy-degradable LFUS-pretreated feed sludge had gradually altered the microbial community by selecting Bacteroidales hydrolyzer with greater metabolic capability to hydrolyze cellulosic biomass without substrate attachment. Meanwhile, Thermotogales with excellent cell mobility for nutrient capturing was highly active within the community. Foremost proportion of the methanogenesis was contributed by the dominant Methanomicrobiales via carbon dioxide reduction. More interestingly, a perceivable proportion of the reverse electron flow of the community was input from Methanoculleus species other than syntrophic acetate-oxidizing bacteria. In addition, metagenomic binning retrieved several interesting novel metagenomic-assembled genomes (MAGs): MAG-bin6 of Alistipes shahii showed exceptional transcriptional activities towards protein degradation and MAG-bin11 of Candidatus Cloacimonetes with active cellulolytic GH74 gene detected.

CONCLUSIONS

In summary, despite the unchanged sludge digestibility, the applied part-stream LFUS pretreatment strategy was robust in adjusting the microbial pathways towards more effective substrate conversion enabled by free-living hydrolyser and beta-oxidation-capable methanogens.