Nexus between the microbial diversity level and the stress tolerance within the biogas process

Magnetite-based nanoparticles and nanocomposites for recovery of overloaded anaerobic digesters

The effect of magnetite nanoparticles and nanocomposites (magnetite nanoparticles impregnated into graphene oxide) supplement on the recovery of overloaded laboratory batch anaerobic reactors was assessed using two types of starting inoculum: anaerobic granular sludge (GS) and flocculent sludge (FS). Both nanomaterials recovered methane production at a dose of 0.27 g/L within 40 days in GS. Four doses of magnetite nanoparticles from 0.075 to 1 g/L recovered the process in FS systems between 30 and 50 days relaying on the dose. The presence of nanomaterials helped to reverse the effect of volatile fatty acids inhibition and enabled microbial communities to recover but also favoured the development of certain microorganisms over others. In GS reactors, the methanogenic population changed from being mostly acetoclastic (Methanothrix soehngenii) to being dominated by hydrogenotrophic species (Methanobacterium beijingense). Nanomaterial amendment may serve as a preventative measure or provide an effective remedial solution for system recovery following overloading.

Co-substrate composition is critical for enrichment of functional key species and for process efficiency during biogas production from cattle manure

Cattle manure has a low energy content and high fibre and water content, limiting its value for biogas production. Co-digestion with a more energy-dense material can improve the output, but the co-substrate composition that gives the best results in terms of degree of degradation, gas production and digestate quality has not yet been identified. This study examined the effects of carbohydrate, protein and fat as co-substrates for biogas production from cattle manure. Laboratory-scale semi-continuous mesophilic reactors were operated with manure in mono-digestion or in co-digestion with egg albumin, rapeseed oil, potato starch or a mixture of these, and chemical and microbiological parameters were analysed. The results showed increased gas yield for all co-digestion reactors, but only the reactor supplemented with rapeseed oil showed synergistic effects on methane yield. The reactor receiving potato starch indicated improved fibre degradation, suggesting a priming effect by the easily accessible carbon. Both these reactors showed increased species richness and enrichment of key microbial species, such as fat-degrading Syntrophomonadaceae and families known to include cellulolytic bacteria. The addition of albumin promoted enrichment of known ammonia-tolerant syntrophic acetate- and potential propionate-degrading bacteria, but still caused slight process inhibition and less efficient overall degradation of organic matter in general, and of cellulose in particular.

Microbial community development during syngas methanation in a trickle bed reactor with various nutrient sources

Microbial community development within an anaerobic trickle bed reactor (TBR) during methanation of syngas (56% H₂, 30% CO, 14% CO₂) was investigated using three different nutrient media: defined nutrient medium (241 days), diluted digestate from a thermophilic co-digestion plant operating with food waste (200 days) and reject water from dewatered digested sewage sludge at a wastewater treatment plant (220 days). Different TBR operating periods showed slightly different performance that was not clearly linked to the nutrient medium, as all proved suitable for the methanation process. During operation, maximum syngas load was 5.33 L per L packed bed volume (pbv) & day and methane (CH₄) production was 1.26 L CH₄/L_pbv/d. Microbial community analysis with Illumina Miseq targeting 16S rDNA revealed high relative abundance (20-40%) of several potential syngas and acetate consumers within the genera Sporomusa, Spirochaetaceae, Rikenellaceae and Acetobacterium during the process. These were the dominant taxa except in a period with high flow rate of digestate from the food waste plant. The dominant methanogen in all periods was a member of the genus Methanobacterium, while Methanosarcina was also observed in the carrier community. As in reactor effluent, the dominant bacterial genus in the carrier was Sporomusa. These results show that syngas methanation in TBR can proceed well with different nutrient sources, including undefined medium of different origins. Moreover, the dominant syngas community remained the same over time even when non-sterilised digestates were used as nutrient medium. KEY POINTS: • Independent of nutrient source, syngas methanation above 1 L/L_pbv/D was achieved. • Methanobacterium and Sporomusa were dominant genera throughout the process. • Acetate conversion proceeded via both methanogenesis and syntrophic acetate oxidation.

Long-Term, Simultaneous Impact of Antimicrobials on the Efficiency of Anaerobic Digestion of Sewage Sludge and Changes in the Microbial Community

The aim of this study was to evaluate the influence of simultaneous, long-term exposure to increasing concentrations of three classes of antimicrobials (β-lactams, fluoroquinolones and nitroimidazoles) on: (1) the efficiency of anaerobic digestion of sewage sludge, (2) qualitative and quantitative changes in microbial consortia that participate in methane fermentation, and (3) fate of antibiotic resistance genes (ARGs). Long-term supplementation of sewage sludge with a combination of metronidazole, amoxicillin and ciprofloxacin applied at different doses did not induce significant changes in process parameters, including the concentrations of volatile fatty acids (VFAs), or the total abundance of ARGs. Exposure to antibiotics significantly decreased methane production and modified microbial composition. The sequencing analysis revealed that the abundance of OTUs characteristic of Archaea was not correlated with the biogas production efficiency. The study also demonstrated that the hydrogen-dependent pathway of methylotrophic methanogenesis could significantly contribute to the stability of anaerobic digestion in the presence of antimicrobials. The greatest changes in microbial biodiversity were noted in substrate samples exposed to the highest dose of the tested antibiotics, relative to control. The widespread use of antimicrobials increases antibiotic concentrations in sewage sludge, which may decrease the efficiency of anaerobic digestion, and contribute to the spread of antibiotic resistance (AR).

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community

Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants

There are almost 9500 biogas plants in Germany, which are predominantly operated with energy crops and residues from livestock husbandry over the last two decades. In the future, biogas plants must be enabled to use a much broader range of input materials in a flexible and demand-oriented manner. Hence, the microbial communities will be exposed to frequently varying process conditions, while an overall stable process must be ensured. To accompany this transition, there is the need to better understand how biogas microbiomes respond to management measures and how these responses affect the process efficiency. Therefore, 67 microbiomes originating from 49 agricultural, full-scale biogas plants were taxonomically investigated by 16S rRNA gene amplicon sequencing. These microbiomes were separated into three distinct clusters and one group of outliers, which are characterized by a specific distribution of 253 indicative taxa and their relative abundances. These indicative taxa seem to be adapted to specific process conditions which result from a different biogas plant operation. Based on these results, it seems to be possible to deduce/assess the general process condition of a biogas digester based solely on the microbiome structure, in particular on the distribution of specific indicative taxa, and without knowing the corresponding operational and chemical process parameters. Perspectively, this could allow the development of detection systems and advanced process models considering the microbial diversity.

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP

Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.

Microbial mechanism of enhancing methane production from anaerobic digestion of food waste via phase separation and pH control

Phase separation and pH control are commonly used to improve methane production during anaerobic digestion (AD) of food waste, but their influencing mechanisms have not been fully discovered through microbial analysis. In this study, single-phase AD (SPAD), two-phase AD without pH control (TPAD-pHUC), and TPAD with fermentation pH controlled at 6.0 and 4.5 were conducted. The results showed that phase separation decreased the ratio of total bacteria to total archaea in the methanogenic phase. At the organic loading rate (OLR) of 1.9 g/(L·d), methanogenesis was dominated by acetoclastic Methanosaeta in both SPAD and TPAD-pHUC, while elevated Methanoculleus and active hydrogen production initiated a shift from the acetoclastic to hydrogenotrophic pathway in SPAD as OLR increased, eventually resulting in excessive acidification at OLR 3.2 g/(L·d). TPAD-pHUC was dominated by Methanosaeta with scarce hydrogen production genes, and thus maintained a delicate balance between fewer acidogens and methanogens at OLR 3.2-3.7 g/(L·d). TPAD with pH control exhibited higher methane yield (460-482 ml/g) at OLR 1.9 g/(L·d) due to the enhancement of protein degradation and the conversion from methylated compounds to methane by Methanosarcina. High Na⁺ concentration facilitated the proliferation of hydrogen production bacteria, but inhibited acetoclastic methanogenesis at OLR 2.4 g/(L·d). In comparison with SPAD and pH control, TPAD without pH control, integrating 4 d acidogenesis and 22 d methanogenesis, exhibited the best and steady performance at OLR 3.7 g/(L·d) with methane production exceeding 370 ml/g.

Post-treatment of dewatered digested sewage sludge by thermophilic high-solid digestion for pasteurization with positive energy output

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH₄/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19-29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS.

Ammonia-induced inhibition of manure-based continuous biomethanation process under different organic loading rates and associated microbial community dynamics

Three Continuously Stirred Tank Reactors (CTSRs) were operating at steady state conditions with Organic Loading Rates (OLR) of 2.09, 3.024 and 4.0 g VS L^-1 d^-1. Glucose was used as the sole factor for increasing the OLR, linking the increase of the OLR with the C/N ratio increase. The reactors were stressed by increasing the ammonia concentration to 5 g L^-1 from 1.862 g L^-1. The results showed elevating inhibition of the anaerobic process by increasing the C/N ratio just by increasing the OLR, under the high ammonia concentration. A different response of the bacterial and archaeal community under ammonia stressed conditions was also observed. Under the high ammonia concentration, hydrogen-depended methylotrophic was the dominant methanogenesis route at OLR of 2.09 g VS L^-1d^-1, while the hydrogenotrophic route was the dominant at the high OLR of 4 g VS L^-1d^-1, which coincided with high acetate and propionate concentrations.

Direct inoculation of a biotrickling filter for hydrogenotrophic methanogenesis

Hydrogenotrophic biomethanation in a biotrickling filter has been reported to be a proven technology for biological biogas upgrading in recent studies. However, the preparation of enriched hydrogenotrophic methanogens in a separate reactor prior to biomethanation in a trickled bed is a lengthy procedure and therefore hard to apply on an industrial scale. This study explored the direct inoculation of anaerobic biogas digestate for simultaneous enrichment of hydrogenotrophic methanogens and biofilm immobilisation in a trickled bed system. The direct inoculation and formation of hydrogenotrophic biofilm was successful and resulted in a stable H₂ loading rate of 11  [Formula: see text] , with the highest specific methane productivity recorded at 3.03 Nm³m_R^-3d^-1 and a purity of 98% CH₄ in thermophilic conditions. The DNA analysis confirmed that hydrogenotrophic methanogens dominated the archaeal consortia.

Survey of microbes in industrial-scale second-generation bioethanol production for better process knowledge and operation

The microbes present in bioethanol production processes have been previously studied in laboratory-scale experiments, but there is a lack of information on full-scale industrial processes. In this study, the microbial communities of three industrial bioethanol production processes were characterized using several methods. The samples originated from second-generation bioethanol plants that produce fuel ethanol from biowaste, food industry side streams, or sawdust. Amplicon sequencing targeting bacteria, archaea, and fungi was used to explore the microbes present in biofuel production and anaerobic digestion of wastewater and sludge. Biofilm-forming lactic acid bacteria and wild yeasts were identified in fermentation samples of a full-scale plant that uses biowaste as feedstock. During the 20-month monitoring period, the anaerobic digester adapted to the bioethanol process waste with a shift in methanogen profile indicating acclimatization to high concentrations of ammonia. Amplicon sequencing does not specifically target living microbes. The same is true for indirect parameters, such as low pH, metabolites, or genes of lactic acid bacteria. Since rapid identification of living microbes would be indispensable for process management, a commercial method was tested that detects them by measuring the rRNA of selected microbial groups. Small-scale testing indicated that the method gives results comparable with plate counts and microscopic counting, especially for bacterial quantification. The applicability of the method was verified in an industrial bioethanol plant, inspecting the clean-in-place process quality and detecting viability during yeast separation. The results supported it as a fast and promising tool for monitoring microbes throughout industrial bioethanol processes.

Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants

Efforts to integrate biogas plants into bioeconomy concepts will lead to an expansion of manure-based (small) biogas plants, while their operation is challenging due to critical characteristics of some types of livestock manure. For a better process understanding, in this study, three manure-based small biogas plants were investigated with emphasis on microbiome diversity. Due to varying digester types, feedstocks, and process conditions, 16S rRNA gene amplicon sequencing showed differences in the taxonomic composition. Dynamic variations of each investigated biogas plant microbiome over time were analyzed by terminal restriction fragment length polymorphism (TRFLP), whereby nonmetric multidimensional scaling (NMDS) revealed two well-running systems, one of them with a high share of chicken manure, and one unstable system. By using Threshold Indicator Taxa Analysis (TITAN), community-level change points at ammonium and ammonia concentrations of 2.25 g L^-1 and 193 mg L^-1 or volatile fatty acid concentrations of 0.75 g L^-1were reliably identified which are lower than the commonly reported thresholds for critical process stages based on chemical parameters. Although a change in the microbiome structure does not necessarily indicate an upcoming critical process stage, the recorded community-level change points might be a first indication to carefully observe the process.

Comparative study of industrial-scale high-solid biogas production from food waste: Process operation and microbiology

Anaerobic high-solid treatment (HST) for processing food waste and biogas production is a viable technology with considerable commercial potential. In this study, we examined and compared mesophilic and thermophilic industrial-scale plug-flow digesters. The HSTs demonstrated reasonable biogas yields from food waste (0.4-0.6 Nm³ CH₄/kg volatile solids). However, during operation at thermophilic conditions ammonia inhibition (~2 g NH₃-N/L) and acid accumulation (6-14 g/L) caused severe process disturbance. Microbial community structures diverged between the processes, with temperature appearing to be a strong driver. A unique feature of the thermophilic HSTs was high abundance of the uncultivated Clostridia group MBA03 and temperature fluctuations in one mesophilic HST were linked to drastically decreased abundance of methanogens and relative abundance of Cloacimonetes. The process data obtained in this study clearly demonstrate both potential and challenges in HST of food waste but also possibilities for management approaches to tackle process imbalance and restore process function.

Effect of a Profound Feedstock Change on the Structure and Performance of Biogas Microbiomes

In this study the response of biogas-producing microbiomes to a profound feedstock change was investigated. The microbiomes were adapted to the digestion of either 100% sugar beet, maize silage, or of the silages with elevated amounts of total ammonium nitrogen (TAN) by adding ammonium carbonate or animal manure. The feedstock exchange resulted in a short-range decrease or increase in the biogas yields according to the level of chemical feedstock complexity. Fifteen taxa were found in all reactors and can be considered as generalists. Thirteen taxa were detected in the reactors operated with low TAN and six in the reactors with high TAN concentration. Taxa assigned to the phylum Bacteroidetes and to the order Spirochaetales increased with the exchange to sugar beet silage, indicating an affinity to easily degradable compounds. The recorded TAN-sensitive taxa (phylum Cloacimonetes) showed no specific affinity to maize or sugar beet silage. The archaeal community remained unchanged. The reported findings showed a smooth adaptation of the microbial communities, without a profound negative impact on the overall biogas production indicating that the two feedstocks, sugar beet and maize silage, potentially do not contain chemical compounds that are difficult to handle during anaerobic digestion.

Metabolic performance of anaerobic digestion of chicken manure under wet, high solid, and dry conditions

The anaerobic digestion (AD) of chicken manure as a solo substrate has been challenging due to the ammonium inhibition effects when adopting a high organic loading rate (OLR). In this study, through increasing both the total solid in the feeding materials from 5% to 20%, and the OLR from 1.7 to 7.1 g-volatile solids (VS)/(L·d), the AD of chicken manure under wet, high solid, and dry conditions, with a fixed hydraulic retention time of 20 days, was investigated. The results obtained indicated that the wet AD system could achieve a methane yield of 0.28 L/g-VS and a low volatile fatty acid level. However, the process deteriorated under dry conditions, and methane formed mainly through acetate oxidation and methanogenesis. Methanosarcina and Methanoplasma were found to be more tolerant But, whether the dry AD of chicken manure can survive an ammonia-stressed environment when the OLR is lowered, still needs investigation.

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H2), ammonium/ammonia (NH4+/NH3) or hydrogen sulphide (H2S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided.