Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage

A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.

Impact of benzalkonium chloride on anaerobic granules and its long-term effects on reactor performance

This study assessed the inhibitory and performance-degrading effects induced by the cationic surfactant benzalkonium chloride (BAC) on anaerobic granules during the long-term operation of a laboratory-scale expanded granular sludge bed (EGSB) reactor. To address the critical scientific problem of how BAC affects the efficiency of EGSB reactors, this research uniquely evaluated the long-term stress response to BAC by systematically comparing continuous and discontinuous inhibitor exposure scenarios. The novel comparison demonstrated that inhibitor concentration is of minor relevance compared to the biomass-specific cumulative inhibitor load in the reactor. After exceeding a critical biomass-specific cumulative inhibitor load of 6.1-6.5 mg BAC/g VS, continuous and discontinuous exposure to BAC caused comparable significant deterioration in reactor performance, including accumulation of volatile fatty acids (VFA), decreased removal efficiency, reduced methane production, as well as the wash-out, flotation, and disintegration of anaerobic granules. BAC exposures had a more detrimental effect on methanogenesis than on acidogenesis. Moreover, long-term stress by BAC led to an inhibition of protein production, resulting in a decreased protein-to-polysaccharide ratio of extracellular polymeric substances (EPS) that promoted destabilizing effects on the granules. Finally, hydrogenotrophic methanogenesis was triggered. Reactor performance could not be restored due to the severe loss of granular sludge.

Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches

The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.

Complexity of temperature dependence in methanogenic microbial environments

There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH₄, an important greenhouse gas. Microbial CH₄ production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO₂ and CH₄. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH₄ production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H₂/CO₂ as immediate CH₄ precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH₄ production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (E_a). Interestingly, CH₄ release from defined microbial cultures, from environmental samples and from wetland field sites all show similar E_a values around 100 kJ mol^-1 indicating that CH₄ production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.

A high-value biohythane production: Feedstocks, reactor configurations, pathways, challenges, technoeconomics and applications

In recent years, the demand for high-quality biofuels from renewable sources has become an aspirational goal to offer a clean environment by alternating the depleting fossil fuels to meet future energy needs. In this aspect, biohythane production from wastes has received extensive research interest since it contains superior fuel characteristics than the promising conventional biofuel i.e. biogas. The main aim is to promote research and potentials of biohythane production by a systematic review of scientific literature on the biohythane production pathways, substrate/microbial consortium suitability, reactor design, and influential process/operational factors. Reactor configuration also decides the product yield in addition to other key factors like waste composition, temperature, pH, retention time and loading rates. Hence, a detailed emphasis on different reactor configurations with respect to the type of feedstock has also been given. The technical challenges are highlighted towards process optimization and system scale up. Meanwhile, solutions to improve product yield, technoeconomics, applications and key policy and governance factors to build a hydrogen based society have also been discussed.

Novel nitrogen-doped biochar supported magnetite promotes anaerobic digestion: Material characterization and metagenomic analysis

Although different conductive materials have been applied to anaerobic digestion, there has not been a material that can really combine their merits and make up their shortcoming from each other. In this study, a novel nitrogen-doped biochar supported magnetite (Fe₃O₄@N-BC) was synthesized. Various material characterizations confirmed that nitrogen atoms were successful doped into the biochar and magnetite precipitated on its surface. 5 g/L Fe₃O₄@N-BC achieved the highest promotion of cumulative CH₄ production by 1.75 times compared with the blank group. Further metagenomic analysis revealed that Fe₃O₄@N-BC could increase the gene abundances of pilA, MmcA, Fpo, Rnf and HdrEd in bacteria Clotridium, Pseudomonas and Syntrophomonas and archaea Methanosarcina. Redundancy analysis showed that it was electrical conductivity and electron exchange capacity that were the key physicochemical characteristics for Fe₃O₄@N-BC to facilitating direct interspecies electron transfer. This study provides a reference for future conductive material synthesis and its application for anaerobic digestion.

Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States

BACKGROUND

During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal.

OBJECTIVE

Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities.

METHODS

In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods.

RESULTS

Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities).

CONCLUSIONS

Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.

Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge

Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.

Obstacles faced by methanogenic archaea originating from substrate-driven toxicants in anaerobic digestion

Anaerobic digestion (AD) is used to treat waste and produce bioenergy. However, toxicants, which originate from the substrate, can inhibit or damage the digestion process. Methanogenic archaea (MA), which are the executor in the methanogenesis stage, are more sensitive than bacteria to these toxicants. This review discusses the effects of substrate-driven toxicants, namely, antibiotics, H₂S and sulfate, heavy metals (HMs), long-chain fatty acids (LCFAs), and ammonia nitrogen, on the activity of MAs, methanogenic pathways, and the inter-genus succession of MAs. The adverse effects of these five toxicants on MA include effects on pH, damages to cell membranes, the prevention of protein synthesis, changes in hydrogen partial pressure, a reduction in the bioavailability of trace elements, and hindrance of mass transfer. These effects cause a reduction in MA activity and the succession of MAs and methanogenic pathways, which affect AD performance. Under the stress of these toxicants, succession occurs among HA (hydrogenotrophic methanogen), AA (acetoclastic methanogen), and MM (methylotrophic methanogen), especially HA gradually replaces AA as the dominant MA. Simultaneously, the dominant methanogenic pathway also changes from the aceticlastic pathway to other methanogenic pathways. A comprehensive understanding of the impact of toxicants on MA permits more specific targeting when developing strategies to mitigate or eliminate the effects of these toxicants.

Commercial formulation amendment transiently affects the microbial composition but not the biogas production of a full scale methanogenic UASB reactor

The treatment of dairy wastewater in methanogenic reactors cause several problems due to their high lipid content. One strategy to overcome these problems is the use of commercial formulations. Here we studied the effect of adding a commercial formulation, designed to improve fat degradation, on both the microbial community composition and reactor performance. Samples from two full-scale Up-flow Anaerobic Sludge Blanket (UASB) reactors in parallel arrangement were analysed. The commercial product was added to one of the reactors while the other was used as control. The amendment increased significantly the fat removal but an accumulation of volatile fatty acids was detected. Nevertheless, no significant differences were observed in the total Chemical Oxygen Demand (COD) removal and biogas production between reactors. A significant change in the bacterial community was not detected by 16S rRNA gene Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis probably due to the limitation of the technique. A strong change in the composition of the phylum Firmicutes was detected with 16S rRNA gene amplicon sequencing; however, it didn't persist during the whole operation period. The relative abundance of minor Operational Taxonomic Units (OTUs) with sequences related to syntrophic bacteria increased with the amendment. Although a better hydrolytic capacity was obtained when adding the commercial product, the overall process did not improve and no increase in biogas production was detected. Alternative strategies could be applied to avoid the accumulation of intermediary products and improve biogas production as intermittent addition of the commercial product or batch operation of reactors.

Pyrite formation from FeS and H2S is mediated through microbial redox activity

Pyrite is the most abundant iron−sulfur mineral in sediments. Over geological times, its burial controlled oxygen levels in the atmosphere and sulfate concentrations in seawater. However, the mechanism of pyrite formation in sediments is still being debated. We show that lithotrophic microorganisms can mediate the transformation of FeS and H₂S to FeS₂ at ambient temperature if metabolically coupled to methane-producing archaea. Our results provide insights into a metabolic relationship that could sustain part of the deep biosphere and lend support to the iron−sulfur-world theory that postulated FeS transformation to FeS₂ as a key energy-delivering reaction for life to emerge.

The exergonic reaction of FeS with H₂S to form FeS₂ (pyrite) and H₂ was postulated to have operated as an early form of energy metabolism on primordial Earth. Since the Archean, sedimentary pyrite formation has played a major role in the global iron and sulfur cycles, with direct impact on the redox chemistry of the atmosphere. However, the mechanism of sedimentary pyrite formation is still being debated. We present microbial enrichment cultures which grew with FeS, H₂S, and CO₂ as their sole substrates to produce FeS₂ and CH₄. Cultures grew over periods of 3 to 8 mo to cell densities of up to 2 to 9 × 10⁶ cells per mL⁻¹. Transformation of FeS with H₂S to FeS₂ was followed by ⁵⁷Fe Mössbauer spectroscopy and showed a clear biological temperature profile with maximum activity at 28 °C and decreasing activities toward 4 °C and 60 °C. CH₄ was formed concomitantly with FeS₂ and exhibited the same temperature dependence. Addition of either penicillin or 2-bromoethanesulfonate inhibited both FeS₂ and CH₄ production, indicating a coupling of overall pyrite formation to methanogenesis. This hypothesis was supported by a 16S rRNA gene-based phylogenetic analysis, which identified at least one archaeal and five bacterial species. The archaeon was closely related to the hydrogenotrophic methanogen Methanospirillum stamsii, while the bacteria were most closely related to sulfate-reducing Deltaproteobacteria, as well as uncultured Firmicutes and Actinobacteria. Our results show that pyrite formation can be mediated at ambient temperature through a microbially catalyzed redox process, which may serve as a model for a postulated primordial iron−sulfur world.

Trichococcus shcherbakoviae sp. nov., isolated from a laboratory-scale anaerobic EGSB bioreactor operated at low temperature

A new species of the genus Trichococcus, strain Art1^T, was isolated from a psychrotolerant syntrophic propionate-oxidizing consortium, obtained before from a low-temperature EGSB reactor fed with a mixture of VFAs (acetate, propionate and butyrate). The 16S rRNA gene sequence of strain Art1^T was highly similar to those of other Trichococcus species (99.7-99.9 %) but digital DNA-DNA hybridization values were lower than those recommended for the delineation of a novel species, indicating that strain Art1^T is a novel species of the genus Trichococcus. Cells of strain Art1^T are non-motile cocci with a diameter of 0.5-2.0 µm and were observed singularly, in pairs, short chains and irregular conglomerates. Cells of Art1^T stained Gram-positive and produced extracellular polymeric substances . Growth was optimal at pH 6-7.5 and cells could grow in a temperature range of from -2 to 30 °C (optimum 25-30 °C). Strain Art1^T can degrade several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate and ethanol. The genomic DNA G+C content of strain Art1^T is 46.7 %. The major components of the cellular fatty acids are C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c. Based on genomic and physiological characteristics of strain Art1^T, a new species of the genus Trichococcus, Trichococcusshcherbakoviae, is proposed. The type strain of Trichococcusshcherbakoviae is Art1^T (=DSM 107162^T = VKM B-3260^T).

Evaluation of process performance and retained sludge properties of a psychrophilic UASB reactor for treatment of iso-plophyl alcohol (2-propanol)-containing wastewater

In this study, a continuous feeding experiment was conducted with synthetic iso-plophyl alcohol (2-propanol)-containing wastewater using a lab-scale psychrophilic UASB reactor to evaluate process performance and retained sludge properties. For smooth acclimation, methanogenic granular sludge was seeded and a proportion of 2-propanol in the synthetic wastewater containing sucrose and volatile fatty acids was increased stepwise from 0% to 30%, 60% and then 90% of COD (chemical oxygen demand). As a result, after a 4-week period for acclimation to 2-propanol degradation, a COD removal rate of 95% was achieved at an organic loading rate (OLR) of 8.4 kg COD/m³/day. Additionally, the physical properties of the retained granular sludge were maintained even when the reactor was supplied with 2-propanol-rich wastewater for more than 200 days. From the batch assays using serum bottles, methanogenic degradation of 2-propanol was observed with acetone accumulation. By comparison, 2-propanol degradation was clearly inhibited in the presence of chloroform as a specific inhibitor of methanogen. A domain archaeal community structure analysis targeting 16S rRNA genes showed the relative abundance of the genus Methanospillium was increased in the 2-propanol acclimated sludge. These results suggested Methanospillium related species in the granular sludge appreciably contributed to the direct degradation of 2-proapanol into acetone under an anaerobic condition.

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: Methane production and microbial community in CSTR process

Based on continuous anaerobic co-digestion of cow manure with available carbon slowly released corn straw, the effect of adding available carbon quickly released fruit and vegetable waste (FVW) was explored, meanwhile microbial community variation was studied in this study. When the FVW added was 5% and 1%, the methane production of the cow manure and corn straw was improved, and the start-up process was shortened. With higher proportion of FVW to 5%, the performance was superior with a mean methane yield increase of 22.4%, and a greater variation of bacterial communities was observed. FVW enhanced the variation of the bacterial communities. The microbial community structure changed during fermentation and showed a trend toward a diverse and balance system. Therefore, the available carbon quickly released FVW was helpful to improve the anaerobic co-digestion of the cow manure and available carbon slowly released corn straw.

Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea

We examined the effect of ammonium and temperature on methane production in high rate upflow anaerobic sludge bed reactors treating pig manure supernatant. We operated four reactors at two ammonium concentrations (‘low’ at 1.9, ‘high’ at 3.7 g L⁻¹, termed LA and HA reactors, respectively) and at variable temperatures over 358 days. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons. Ammonium was a major selective factor for bacterial and archaeal community structure. After ~200 days of adaptation to high ammonium levels, acetate and propionate removal and methane production improved substantially in HA reactors. Aceticlastic Methanosaeta was abundant and positively correlated to methane yield in the HA reactors, whereas Methanosarcina was more abundant in LA reactors. Furthermore, a group of monophyletic OTUs that was related to Thaumarchaeota in phylogenetic analysis was highly abundant in the archaeal communities, particularly in the HA reactors. The most abundant bacterial OTU in LA reactors, representing Syntrophomonadaceae, was also positively correlated to methane yield in the HA reactors, indicating its importance in methane production under ammonia stress. In conclusion, efficient methane production, involving aceticlastic methanogenesis by Methanosaeta took place in the reactors at free ammonia concentrations as high as 1 g L⁻¹.

Method for Indirect Quantification of CH4 Production via H2O Production Using Hydrogenotrophic Methanogens

Hydrogenotrophic methanogens are an intriguing group of microorganisms from the domain Archaea. Methanogens exhibit extraordinary ecological, biochemical, and physiological characteristics and possess a huge biotechnological potential. Yet, the only possibility to assess the methane (CH₄) production potential of hydrogenotrophic methanogens is to apply gas chromatographic quantification of CH₄. In order to be able to effectively screen pure cultures of hydrogenotrophic methanogens regarding their CH₄ production potential we developed a novel method for indirect quantification of the volumetric CH₄ production rate by measuring the volumetric water production rate. This method was established in serum bottles for cultivation of methanogens in closed batch cultivation mode. Water production was estimated by determining the difference in mass increase in a quasi-isobaric setting. This novel CH₄ quantification method is an accurate and precise analytical technique, which can be used to rapidly screen pure cultures of methanogens regarding their volumetric CH₄ evolution rate. It is a cost effective alternative determining CH₄ production of methanogens over CH₄ quantification by using gas chromatography, especially if applied as a high throughput quantification method. Eventually, the method can be universally applied for quantification of CH₄ production from psychrophilic, thermophilic and hyperthermophilic hydrogenotrophic methanogens.

Effect of steam explosion pretreatment on the anaerobic digestion of rice straw

Steam explosion pretreatment on the anaerobic digestion of rice straw.

Biologically Produced Methane as a Renewable Energy Source

Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO₂. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person.

Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies

Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.