The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture

Soil drying legacy does not affect phenanthrene fate in soil but modifies bacterial community response

Alteration of the structure of soil microbial communities following the elimination of hydrophobic organic pollutants (e.g., polycyclic aromatic hydrocarbons, PAHs) is generally assessed using DNA-based techniques, and soil is often required to dry prior to pollutant addition, to facilitate a better mix when establishing microcosms. However, the drying practice may have a legacy effect on soil microbial community structure, which would in turn influence the biodegradation process. Here, we used ¹⁴C-labeled phenanthrene to examine the potential side effects of precedent short-term drought events. The results indicate that the drying practice had legacy effects on soil microbial community structure, illustrated by irreversible shifts in the communities. The legacy effects had no significant impact on phenanthrene mineralization and non-extractable residue formation. However, they altered the response of bacterial communities to PAH degradation, leading to a decrease in the abundance of potential PAH degradation genes plausibly attributed to moderately abundant taxa. Based on a comparison of the varied effects of different drying intensity levels, an accurate description of microbial responses to phenanthrene degradation strongly relies on the establishment of stable microbial communities before PAH amendment. Concurrent alterations in the communities resulting from environmental perturbation could greatly mask minor alterations from the degradation of recalcitrant hydrophobic PAH. In practice, to minimize the legacy effects, a soil equilibration step with a reduced drying intensity is indispensable.

Effect of Endogenous Methane Production: A Step Forward in the Validation of Biochemical Methane Potential (BMP) Tests

This work evaluates the influence of the inoculum type, the pre-consumption of the residual substrate and the ratio of blanks’ headspace volume to working volume (Hv Wv−1, 0.6 to 10) on Biochemical Methane Potential (BMP) measurements when methane is monitored by gas chromatography. Different inocula were tested: digested sewage sludge—DSS, granular sludge—GS and fresh dairy manure—DM. Microcrystalline cellulose was used as the substrate. BMP surpassed the maximum theoretical value (BMPmax = 414 L kg−1) when methane produced in the blanks was not discounted, showing that degassing cannot stand alone as an alternative to the procedure of discounting the inoculum’s background production. Still, when the residual substrate concentration is high (e.g., in DM), degassing is mandatory because methane produced from its digestion will conceal the methane produced from the substrate in the BMP determination. For inocula with a low residual substrate (e.g., GS), short degassing periods are recommended in order to avoid detrimental effects on methanogenic activity. For moderate residual substrate concentrations (e.g., DSS), BMP values closer to BMPmax (90–97%) were achieved after degassing and discounting the blanks with lower Hv Wv−1. For higher Hv ∙ Wv−1, less accurate quantification occurred, likely due to error propagation. Proper inoculum pre-incubation time and discounting the methane production from blanks with low Hv Wv−1 (adjusted according to the estimated background methane) are essential for accurate BMP determinations.

Prediction of methane production from co-digestion of lignocellulosic biomass with sludge based on the major compositions of lignocellulosic biomass

In the present study, the simplex lattice mixture design method was adopted to design the artificial biomass with different ratios of three major components (cellulose, hemicellulose, lignin). The methane yield from the co-digestion of the artificial/ natural biomass (corn stover, wheat stover, rice straw, and peanut stalk) samples with the mixed sludge at the mixture ratio of 1:1 based on total solid (TS) content was recorded for 50 days. The original mathematical prediction models for estimating the cumulative methane production, maximum methane production rate, and lag phase time were established based on the experimental results from the co-digestion of artificial biomass with sludge. To investigate the influence of the structural features of biomass and interactions among the components of biomass which contributing to the inhibition of methane production, the macroscopic factor (MF) was proposed. The mathematical models which revealed the relationship between MF and the methane production parameters were developed by the combination of the prediction results from the original mathematical prediction model and experimental results from the co-digestion of natural biomass with sludge. Modification of the original mathematical prediction models was carried out by considering MF. After modification, the relative error (RE) and root mean square error (RMSE) of the prediction model for cumulative methane production were declined from 19.00 to 30.18% and 42.38 mL/g VS_added to that of - 1.93~7.14% and 4.36 mL/g VS_added, respectively.

Measurement of Biochemical Methane Potential of Heterogeneous Solid Substrates: Results of a Two-Phase French Inter-Laboratory Study

Biochemical methane potential (BMP) is essential to determine the production of methane for various substrates; literature shows important discrepancies for the same substrates. In this paper, a harmonized BMP protocol was developed and tested with two phases of BMP tests carried out by eleven French laboratories. Surprisingly, for the three same solid tested substrates (straw; raw mix and dried-shredded mix of potatoes, maize, beef meat and straw; and mayonnaise), the standard deviations of the repeatability and reproducibility inter-laboratory were not enhanced by the harmonized protocol (average of about 25% depending on the substrate), as compared to a previous step where all laboratories used their own protocols. Moreover, statistical analyses of all the results, after removal of the outliers (about 15% of all observations), did not highlight significant effect of the operational effect on BMP (stirring, automatic or manual gas quantification, use of trace metal, uses a bicarbonate buffer, inoculum to substrate ratio) at least for the tested ranges. On the other hand, the average intra-laboratory repeatability was low, about 7%, whatever the protocol, the substrate and the laboratory. It also appears that drying the SA substrate, which contained proteins, carbohydrates, lipids and fibers, does not impact its BMP.

Improving Inter-Laboratory Reproducibility in Measurement of Biochemical Methane Potential (BMP)

Biochemical methane potential (BMP) tests used to determine the ultimate methane yield of organic substrates are not sufficiently standardized to ensure reproducibility among laboratories. In this contribution, a standardized BMP protocol was tested in a large inter-laboratory project, and results were used to quantify sources of variability and to refine validation criteria designed to improve BMP reproducibility. Three sets of BMP tests were carried out by more than thirty laboratories from fourteen countries, using multiple measurement methods, resulting in more than 400 BMP values. Four complex but homogenous substrates were tested, and additionally, microcrystalline cellulose was used as a positive control. Inter-laboratory variability in reported BMP values was moderate. Relative standard deviation among laboratories (RSDR) was 7.5 to 24%, but relative range (RR) was 31 to 130%. Systematic biases were associated with both laboratories and tests within laboratories. Substrate volatile solids (VS) measurement and inoculum origin did not make major contributions to variability, but errors in data processing or data entry were important. There was evidence of negative biases in manual manometric and manual volumetric measurement methods. Still, much of the observed variation in BMP values was not clearly related to any of these factors and is probably the result of particular practices that vary among laboratories or even technicians. Based on analysis of calculated BMP values, a set of recommendations was developed, considering measurement, data processing, validation, and reporting. Recommended validation criteria are: (i) test duration at least 1% net 3 d, (ii) relative standard deviation for cellulose BMP not higher than 6%, and (iii) mean cellulose BMP between 340 and 395 NmLCH4 gVS−1. Evidence from this large dataset shows that following the recommendations—in particular, application of validation criteria—can substantially improve reproducibility, with RSDR < 8% and RR < 25% for all substrates. The cellulose BMP criterion was particularly important. Results show that is possible to measure very similar BMP values with different measurement methods, but to meet the recommended validation criteria, some laboratories must make changes to their BMP methods. To help improve the practice of BMP measurement, a new website with detailed, up-to-date guidance on BMP measurement and data processing was established.

Impact of Storage Conditions on the Methanogenic Activity of Anaerobic Digestion Inocula

The impact of storage temperature (4, 22 and 37 °C) and storage time (7, 14 and 21 days) on anaerobic digestion inocula was investigated through specific methanogenic activity assays. Experimental results showed that methanogenic activity decreased over time with storage, regardless of storage temperature. However, the rate at which the methanogenic activity decreased was two and five times slower at 4 °C than at 22 and 37 °C, respectively. The inoculum stored at 4 °C and room temperature (22 °C) maintained methanogenic activity close to that of fresh inoculum for 14 days (<10% difference). However, a storage temperature of 4 °C is preferred because of the slower decrease in activity with lengthier storage time. From this research, it was concluded that inoculum storage time should generally be kept to a minimum, but that storage at 4 °C could help maintain methanogenic activity for longer.

Foliar micromorphology and its role in identification of the Apocynaceae taxa

In the present study, we evaluate the importance of foliar epidermal micromorphological characteristics of Apocyanaceae for accurate identification and classification. The species were collected from the University of Peshawar's main campus in the spring season to observe its qualitative and quantitative features. The length and width of guard cells, stomatal pore and subsidiary cells, trichomes, and crypts on both sides of the leaf were examined. Many species were observed to be hypostomatic. Plumeria rubra, Raulfia serpentine, Thevetia peruviana, Trachelospermum lucidum, Alstonia scholaris, and Catharanthus roseus demonstrated hypostomatic leaves. Nearly all the investigated species had anisocytic type of stomata only or in combination with other types of stomata on the upper and lower epidermis. Carissa carandas had anomocytic, anisocytic, and cyclocytic type of stomata on the upper epidermis, and the lower epidermis showed variations in stomatal type, such as anomocytic, stephanocytic, brachyparacytic, and hemiparacytic. Nerium oleander had no specific shape of stomata but showed stomatal crypts in which the stomata were enclosed inside many trichomes. The taxonomic key based on stomatal types, epidermal cells, stomatal index value, and statistical analysis, along with the variations in the epidermal cells, shows the link between the selected plants species, which will provide a baseline for future anatomical studies. This study highlights many undocumented micromorphological characteristics. The anatomical characteristics observed in this study will be helpful for taxonomic identification and species delimitation of the family Apocynaceae.

Perspectives on variabilities in biomethane potential test parameters and outcomes: A review of studies published between 2007 and 2018

Biomethane Potential (BMP) test continues to be a useful and inexpensive assay to estimate the digestibility and maximum methane production of various organic substrates in anaerobic digestion or co-digestion processes. Despite its usefulness and several published efforts toward standardizing it, the BMP test still do not follow a universally accepted standard protocol. This makes the comparison of results among studies quite challenging. In this context, this paper analyzes 78 peer-reviewed BMP studies published between 2007 and 2018 that used the BMP test primarily to assess methane potential of commonly digested substrates, such as food waste, wastewater sludge and manure. We focused on the similarities and differences in the methodologies used and, where possible, the results obtained from these studies were compared and discussed. It was observed that many studies do not provide adequate information on salient aspects of the BMP methodology, and results are sometimes reported in different units of measurements. The inoculum to substrate ratio (ISR), substrate concentration and/or load should be clearly indicated in future studies, and positive controls should be included to validate BMP results. It is recommended that more studies assess the impact of nutrient addition, potential effects of continuous and intermittent mixing and mixing intensities and the influence of reactor size and headspace volume on BMP results.

Effect of anaerobic digester inoculum preservation via lyophilization on methane recovery

A robust anaerobic digestion (AD) inoculum is key to a successful digestion process by providing the abundant bacteria needed for converting substrate to useable methane (CH₄). While transporting digester contents from one AD to another for digester startup has been the norm, transportation costs are high, and it is not feasible to transport wet inoculum to remote locations. In this study, the impact of preservation of AD inoculum via lyophilization was investigated for the purposes of digester startup and restabilization. The effect of lyophilizing inoculum on CH₄ production using food waste as the substrate was tested using biochemical methane potential (BMP) tests under the following conditions: (1) three inoculum sources, (2) two inoculum to substrate ratios (ISR), (3) two cryoprotectants, and (4) two inoculum growth phases. After lyophilization with skim milk, the three inocula produced 144-146 mL CH₄/g volatile solids (VS) and 194-225 mL CH₄/g VS at a 2:1 and 4:1 ISR, respectively, with 33-57% more CH₄ at the 4:1 ISR. Preservation with 10% skim milk exhibited complete recovery of CH₄ production, while 10% glycerol and 10% glycerol/skim milk mixture yielded 76% and 4% CH₄ recovery, respectively. Inoculum growth phase before preservation (mid-exponential or stationary growth phase) did not significantly affect CH₄ recovery. The study indicates that inoculum can be preserved via lyophilization using 10% skim milk as a cryoprotectant and reactivated for food waste digestion. The results provide a systematic quantification of the conditions needed to successfully preserve a mixed AD inoculum.

Responses and successions of sulfonamides, tetracyclines and fluoroquinolones resistance genes and bacterial community during the short-term storage of biogas residue and organic manure under the incubator and natural conditions

Biogas residue and organic manure are frequently used for crop planting. However, the evaluation of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial community before their applications to fields is still lacking. This study monitored the variations of bacteria resistant to sulfadiazine, tetracycline and norfloxacin, 57 resistance genes for sulfonamides, tetracyclines and fluoroquinolones as well as the bacterial community during the 28-day aerobic storage of biogas residue and organic manure by using viable plate counts, high-throughput qPCR and Illumina MiSeq sequencing methods. Then two storage conditions, incubator (25 °C) and natural environment, were used to assess the responses of ARB and ARGs to the environmental factors. Results showed that a total of 35 and 21 ARGs were detected in biogas residue and organic manure, respectively. ARB and ARGs were enriched up to 8.01-fold in biogas residue after the 28-day storage, but varied in a narrow range during the storage of organic manure. Compared with the incubator condition, the proliferation of ARB and ARGs in biogas residue under the natural condition was relatively inhibited by the varied and complicated environmental factors. However, we found that there was no significant difference of ARB and ARGs in organic manure between the incubator and natural conditions. Bacterial community was also shifted during the storage of biogas residue, especially Bacteroidetes_VC2.1_Bac22, Aequorivita, Luteimonas and Arenimonas. Network analysis revealed that the relationship in biogas residue was much more complicated than that in organic manure, which ultimately resulted in large successions of ARB and ARGs during the short-term storage of biogas residue. Therefore, we suggest that further measures should be taken before the application of biogas residue to fields.

Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion

Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel. However, this is labor intensive, especially when measuring biogas production. Commercial solutions for multiplying reactors performing continuous anaerobic digestion exist but are expensive and use comparably large reactor volumes, requiring the preparation of substantial amounts of media. Here, a flexible system of Lab-scale Automated and Multiplexed Anaerobic Chemostat system (LAMACs) with a working volume of 200 mL is introduced. Sterile feeding, biomass wasting and pressure monitoring are automated. One module containing six reactors fits the typical dimensions of a lab bench. Thanks to automation, time required for reactor operation and maintenance are reduced compared to traditional lab-scale systems. Several modules can be used together, and so far the parallel operation of 30 reactors was demonstrated. The chemostats are autoclavable. Parameters like reactor volume, flow rates and operating temperature can be freely set. The robustness of the system was tested in a two-month long experiment in which three inocula in four replicates, i.e., twelve continuous digesters were monitored. Statistically significant differences in the biogas production between inocula were observed. In anaerobic digestion, biogas production and consequently pressure development in a closed environment is a proxy for ecosystem performance. The precision of the pressure measurement is thus crucial. The measured maximum and minimum rates of gas production could be determined at the same precision. The LAMACs is a tool that enables us to put in practice the often-demanded need for replication and rigorous testing in microbial ecology as well as bioprocess engineering.

Evaluating analytical methods for the characterization of lipids, proteins and carbohydrates in organic substrates for anaerobic co-digestion

This study provides insights into the characterization of lipids, proteins and carbohydrate content in substrates for codigestion, and evaluates their effects on biogas yield. Among the analytical methods evaluated, the Bligh and Dyer, Hach Total Nitrogen and the Anthrone method were found to be most suitable for lipids, proteins and carbohydrates analysis, respectively. The co-digestibility of ten co-substrate mixes prepared using various volume-to-volume ratios of foodwaste (FW), fats, oils and grease (FOG), and waste activated sludge (WAS) were tested using biomethane potential assays. The three main substrates were mono-digested as well. WAS mono-digestion yielded the lowest methane yield of 118mL CH₄/g VS, while a 50:50 mix of WAS and FOG, containing 85% lipid and 15% protein produced the highest methane yield of 1040mL CH₄/g VS. In general, lipid-rich samples yielded more biogas than samples rich in proteins and carbohydrates. However, samples rich in proteins and carbohydrates had faster biogas production rates.

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester

In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH3-N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor.

IMPORTANCE

Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the β-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane.

Evaluating an anaerobic digestion (AD) feedstock derived from a novel non-source segregated municipal solid waste (MSW) product

In many nations industrial scale AD of non-agricultural waste materials (such as MSW) has not yet reached its full potential, often constrained by the lack of secure, inexpensive, high quality AD feedstocks, and markets for the resulting digestate material. We tested the output material of a high throughput novel industrial process to define its potential as an AD feedstock (based on quality and consistency). This process, designed to circumvent the constraints of source segregation while still generating segregated waste streams, resulted in the production of a temporally homogenous fibrous material with: an average moisture content of 44.2 (±2.33)%; C:N ratio of ∼32.9:1 (±3.46:1), C:P ratio of ∼228:1 and gross calorific value of 17.4 (±0.29)MJ/kg_(DM). This material provided a CH₄ yield of between 201 and 297m³ CH₄/tonne_(DM) (271-401m³CH₄/tonne_(vs)) comparable to commonly used AD feedstocks. Material contaminant levels were temporally consistent (P>0.05), (average values being Cd 0.63 (±0.19), Cu 56.3 (±7.45), Cr^tot 51.4 (±4.41), Hg<0.3, Ni 28.9 (±5.17), Pb 79.2 (±23.71), Zn 202 (±44.5), total polyaromatic hydrocarbons (PAH) 2.2 (±0.3), and total polychlorinated biphenyls (PCB) (<0.2)mg/kg_(DM)). Calculated digestate contaminant levels were below the median contaminant threshold limits for anaerobic digestates of all countries within the European Union i.e. of Cd 3.35, Cu 535, Cr^tot 535, Hg 8.15, Ni 185, Pb 397.5, Zn 2100mg/kg_(DM). We suggest that novel high throughput processes that produce high quality AD feedstocks, may have a place in further diversion of waste from landfill.

Incubation of innovative methanogenic communities to seed anaerobic digesters

The methanogenic communities in alternative inocula and their potential to increase CH₄ production in mesophilic and psychrophilic dairy manure-based anaerobic digesters were examined. Quantitative-PCR and terminal restriction fragment length polymorphism (T-RFLP) profiles were used to determine archaeal and methanogenic community changes when three inocula (wetland sediment (WS), landfill leachate (LL), and mesophilic digestate (MD)) were incubated at 15, 25, and 35 °C for 91 and 196 days. After each incubation period, the inocula were used in biochemical methane potential (BMP) tests at the incubation temperatures. There was no significant correlation between inoculum mcrA gene copy numbers and CH₄ produced in BMP tests, suggesting that population size was not a distinguishing characteristic for predicting CH₄ production. Archaeal composition in LL and WS reactors generally converged with MD reactors after incubation at 25 and 35 °C for 196 days. These MD reactors had high relative abundance of TRF 302, likely Methanosaetaceae, and low acetic acid (0.62-1.61 mM). At 15 °C incubation, most reactors were associated with high acetic acid (1.61-133.6 mM) and dominated by TRF 199, likely Methanosarcinaceae. The LL reactor incubated at 25 °C for 91 days had higher relative abundance of TRF 199 and produced significantly higher CH₄ than WS and MD reactors in BMP test. In the future, it may be possible to create enrichment cultures that favor particular methanogens and use them as inoculum to benefit digesters at low mesophilic temperatures. Our data provides evidence that tailoring the archaeal community could benefit digesters operating under different conditions.