Reorganisation of a mesophilic biogas microbiome as response to a stepwise increase of ammonium nitrogen induced by poultry manure supply

How anaerobic sludge microbiome respond to different concentrations of nitrite, nitrate, and ammonium ions: a comparative analysis

High concentrations of ammonium, nitrite, and nitrate always induce inhibition in anaerobic wastewater treatment. Due to the complexity and vulnerability of the microbial community (especially methanogens) in anaerobic sludge, little is understood about its underlying microbial mechanism under such inhibition. In this study, the shifts of microbial communities in anaerobic sludge under increasing levels of nitrite, nitrate, and ammonium ions were compared. Results show that although half maximal inhibitory concentrations (methanogenesis) were different for nitrite, nitrate, and ammonium ions with EC₅₀ values of 12, 30, and 3000 mg N/L, respectively, bacteria genera Kosmotoga and Brooklawnia dominated in all of the three high-stress inhibitory systems. Network analysis and redundancy analysis (RDA) of the microbial community showed the treatments with nitrate and nitrite ions decreased the modularity of anaerobic microorganisms. RDA showed that specific methanogenic activity was positively related to coenzyme F₄₂₀ under nitrite inhibition (r_p = 0.833, p < 0.05) and closely correlated with viability under nitrate inhibition. Gram-positive and nonmotile Brooklawnia genus showed a negative correlation with physiological characteristics in the ammonia treatments, suggesting its high resistance to ammonia.

Individual Phenolic Acids in Distillery Stillage Inhibit Its Biomethanization

Polyphenols that are abundant in various organic wastes can inhibit anaerobic degradation of these wastes. This study investigated the effect of the concentration of individual phenolic acids (p-OH benzoic, vanillic, ferulic, sinapic, syringic, and p-coumaric acids) and their mixture on the methane potential of distillery stillage. An increase in phenolic acid concentration adversely affected biogas production and composition, as well as the methane-production rate. The inhibition constants for methane production were 0.5–1.0 g/L of individual phenolic acids and 1.5 g/L of the mixture of these acids. At lower concentrations, the phenolic acids were utilized as a carbon source, but the process was impeded when their concentrations exceeded the threshold value, due to their negative effect on microbial growth. When distillery stillage was spiked with vanillic acid, two-phase methane production was observed. Spiking distillery stillage with vanillic, p-coumaric, syringic, or ferulic acids affected anaerobic digestion the most; 2 g/L of these acids completely inhibited methane production. With 4.0 g/L of all individual phenolic acids, no methane production was observed. As the concentration of these phenolic acids increased from 0.5 to 4.0 g/L, the abundance of methanogenic Archaea, in which acetoclastic methanogens predominated, decreased by about 30 times.

Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.

Response of process performance and microbial community to ammonia stress in series batch experiments

To further clarify the key stage and microorganisms responsible for ammonia inhibition instability, three sequential batch experiments were conducted with various ammonia concentrations and different exposure modes. Acetate metabolism was most sensitive to ammonia, however, after continuous ammonia exposure, acetate metabolism was well restored by a shift in dominant microorganisms. In contrast, the metabolism of longer-chain volatile fatty acids (LCVFAs, C₃-C₅) was only inhibited under a high ammonia concentration (≥6000 mg/L), however, once inhibited, continuous exposure neither restored the abundance of functional microbes nor induced new microorganisms to perform metabolic functions. Therefore, LCVFA metabolism was the key stage responsible for process instability under ammonia stress. Moreover, the deterioration of LCVFA metabolism was caused by the inhibition of syntrophic acetogenic bacteria (SAB) induced by total ammonia nitrogen, rather than the feedback inhibition from methanogenesis. That is, SAB were the key microorganisms involved in process instability.

Effect of nitrogen fertilization on the production of biogas from sweet sorghum and maize biomass

The aim of the study was to determine the biogas productivity from selected cultivars of sorghum (Sorghum bicolor Moench) and maize (Zea mays L.) depending on the dose of mineral fertilization with nitrogen. The topic is novelty in the northern Poland area due to the fact that this crop is not very widespread here. The silage samples were derived from two experiments: (1) two factors experiment with sorghum varieties (Arbatax, KWS Maja, Herkules) and two doses of mineral nitrogen fertilization (0 and 150 kg ha^-1N) in split-plot design. (2) one-factor experiment with fodder maize, variety NK Magitop, and two doses of mineral nitrogen fertilization (0 and 150 kg ha^-1N) in a randomized complete block design. The experiment was performed in four replications in the split-plot design. Methane fermentation was carried out under mesophilic conditions. The temperature of the process was 37°C ± 1°C, while pH 7 ± 0.1. The content of total solids in the bioreactor was 7.0%. The composition of the gas produced was measured once a day with the use of an automatic biogas analyser (GFM 416, GasData). The trial was run in triplicate until the daily yield was less than 1% of the cumulative biogas yield [DIN 38 414-S8. Sediments and sediments. Determination of fermentation characteristics; 1985]. Sorghum was characterized by higher average biogas productivity (about 12%), higher methane content in biogas (about 10%), and higher methane productivity (about 43%). It can, therefore, be stated that sorghum represents as an alternative plant to maize for the purpose of biogas production.

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.

Biomethane Potential Test: Influence of Inoculum and the Digestion System

High precision of measurement of methane potential is important for the economic operation of biogas plants in the future. The biochemical methane potential (BMP) test based on the VDI 4630 protocol is the state-of-the-art method to determine the methane potential in Germany. The coefficient of variation (CV) of methane yield was >10% in several previous inter-laboratory tests. The aim of this work was to investigate the effects of inoculum and the digestion system on the measurement variability. Methane yield and methane percentage of five substrates were investigated in a Hohenheim biogas yield test (D-HBT) by using five inocula, which were used several times in inter- laboratory tests. The same substrates and inocula were also tested in other digestion systems. To control the quality of the inocula, the effect of adding trace elements (TE) and the microbial community was investigated. Adding TE had no influence for the selected, well- supplied inocula and the community composition depended on the source of the inocula. The CV of the specific methane yield was <4.8% by using different inocula in one D-HBT (D-HBT1) and <12.8% by using different digestion systems compared to D-HBT1. Incubation time between 7 and 14 days resulted in a deviation in CV of <4.8%.

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.

Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome

The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.

Response of Propionate-Degrading Methanogenic Microbial Communities to Inhibitory Conditions

Propionate is a crucial intermediate during methane fermentation. Investigating the effects of different kinds of inhibitors on the propionate-degrading microbial community is necessary to develop countermeasures for improving process stability. In the present study, under inhibitory conditions (acetate, propionate, sulfide, and ammonium addition), the dynamic changes of the propionate-degrading microbial community from a mesophilic chemostat fed with propionate as the sole carbon source were investigated using high-throughput sequencing of 16S rRNA. Sulfide and/or ammonia inhibited specific species in the microbial community. Compared with Syntrophobacter, Smithella was more resistant to inhibition by sulfide and/or ammonia. However, Syntrophobacter demonstrated greater tolerance than Smithella under acid inhibition conditions. Some genera that had close phylogenetic relationships and similar functions showed similar responses to different inhibitors.

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.

Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.

Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants

The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.

Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion

In this study, microbiomes of 36 full-scale anaerobic digesters originated from 22 different biogas plants were compared by terminal restriction fragment length polymorphism (TRFLP) analysis. Regarding the differences in microbial community composition, a weighting of the environmental parameters could be derived from higher to lower importance as follows: (i) temperature, (ii) TAN and NH₃ concentrations and conductivity, and (iii) the chemical composition of the supplied feedstocks. Biotic interactions between specific bacterial and archaeal community arrangements were revealed, whereby members of the phyla Bacteroidetes and Cloacimonetes combined with the archaeal genus Methanothrix dominated the conversion of homogeneous feedstocks, such as waste water sludge or industrial waste. As most of the detected TRFs were only found in a certain number of anaerobic digestion plants, each plant develops its unique microbiome. The putative rare species, the specialists, are potentially hidden drivers of microbiome functioning as they provide necessary traits under, e.g., process-inconvenient conditions.

Blending based optimisation and pretreatment strategies to enhance anaerobic digestion of poultry manure

Anaerobic digestion of poultry manure is limited by the excessive levels of nitrogen and the high concentration of dry matter. These limitations are usually overcome either by applying procedures to remove nitrogen or by employing pretreatments that allows to solubilise organic matter. In this work, the treatment of poultry manure was enhanced by co-digestion with pig manure through the methodological determination of optimal mixtures combined together with a thermochemical pretreatment coupled to ammonia stripping. The optimum poultry-pig mixture, resulting in a 24%:76% (volume basis) poultry-pig manure, was determined by applying a methodology based on linear programming which calculates the proportions of the blend which returns the maximum methane production while keeping a stable process. Pretreatment batch experiments, consisting of increasing both temperature and pH simultaneously with ammonia stripping process was optimised for a temperature of 90 °C and a pH of 10 resulting in a nitrogen removal efficiency of 72% and a 1.2-fold higher methane production in comparison to the unpretreated mixture. Continuous anaerobic co-digestion of pretreated optimum mixture enhanced the COD removal efficiency by 37% when compared with the treatment of unpretreated feedstock (37% vs 27%, respectively). This study indicates that combining blending optimisation of substrates, thermochemical pretreatments and ammonia stripping procedures prior to anaerobic co-digestion becomes a good strategy to overtake the limitations offered by solid- and nitrogen-rich substrates, such as poultry manure.

Improving methane yield from organic fraction of municipal solid waste (OFMSW) with magnetic rice-straw biochar

Magnetic biochar is a potential economical anaerobic digestion (AD) additive. To better understand the possible role of magnetic biochar for the improvement of biomethanization performance and the retention of methanogens, magnetic biochar fabricated under different precursor concentrations were introduced into organic fraction of municipal solid waste (OFMSW) slurry AD system. Results showed that methane production in AD treatment with magnetic biochar fabricated under 3.2g FeCl₃:100g rice-straw ratio increased by 11.69% compared with control treatment without biochar addition, due to selective enrichment of microorganisms participating in anaerobic digestion on magnetic biochar. AD treatment with magnetic biochar fabricated under 32g FeCl₃:100g rice-straw ratio resulted in 38.34% decreasement of methane production because of the competition of iron oxide for electron. Furthermore, 25% of total methanogens were absorbed on magnetic biochar and can be harvested with magnet, which can offer a potential solution for preventing the methanogens loss in the anaerobic digesters.

Microbial community composition and electricity generation in cattle manure slurry treatment using microbial fuel cells: effects of inoculum addition

Microbial fuel cell (MFC) is a sustainable technology to treat cattle manure slurry (CMS) for converting chemical energy to bioelectricity. In this work, two types of allochthonous inoculum including activated sludge (AS) and domestic sewage (DS) were added into the MFC systems to enhance anode biofilm formation and electricity generation. Results indicated that MFCs (AS + CMS) obtained the maximum electricity output with voltage approaching 577 ± 7 mV (~ 196 h), followed by MFCs (DS + CMS) (520 ± 21 mV, ~ 236 h) and then MFCs with autochthonous inoculum (429 ± 62 mV, ~ 263.5 h). Though the raw cattle manure slurry (RCMS) could facilitate electricity production in MFCs, the addition of allochthonous inoculum (AS/DS) significantly reduced the startup time and enhanced the output voltage. Moreover, the maximum power (1.259 ± 0.015 W/m²) and the highest COD removal (84.72 ± 0.48%) were obtained in MFCs (AS + CMS). With regard to microbial community, Illumina HiSeq of the 16S rRNA gene was employed in this work and the exoelectrogens (Geobacter and Shewanella) were identified as the dominant members on all anode biofilms in MFCs. For anode microbial diversity, the MFCs (AS + CMS) outperformed MFCs (DS + CMS) and MFCs (RCMS), allowing the occurrence of the fermentative (e.g., Bacteroides) and nitrogen fixation bacteria (e.g., Azoarcus and Sterolibacterium) which enabled the efficient degradation of the slurry. This study provided a feasible strategy to analyze the anode biofilm formation by adding allochthonous inoculum and some implications for quick startup of MFC reactors for CMS treatment.

Pathways in bacterial and archaeal communities dictated by ammonium stress in a high solid anaerobic digester with dewatered sludge

Metagenomic comparisons of microbial profiles were conducted to investigate differences between the samples from steady (Day 42), ammonium-adjusting (Day 63), and ammonium-stressed (Day 102) periods during the 110-day operation of a high solid anaerobic digester of sewage sludge. Comparing to the steady period, biogas production was slightly inhibited after ammonium adjustment, during which the microbes showed higher abundance in 6 of the total 22 ammonium-related genes. In addition, among the 19 amino-acid-related genes, 9 genes involved in amino acid generation and utilization were reduced, which partially revealed the reason of deterioration of volatile solids (VSs) degradation following ammonium stress. Furthermore, although the acetoclastic pathway was to some extent inhibited with the decrease of biogas amount and content, no enhancement of genes involved in hydrogenotrophic methanogenesis was observed, elucidating the distinct role of ammonium stress in directing bacterial community structure toward the enhanced syntrophic acetate oxidation reaction.

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure

Anaerobic digestion of high-salinity wastewaters often results in process inhibition due to the susceptibility of the methanogenic archaea. The ability of the microbial community to deal with increased salinity levels is of high importance to ensure process perseverance or recovery after failure. The exact strategy of the microbial community to ensure process endurance is, however, often unknown. In this study, we investigated how the microbial community is able to recover process performance following a disturbance through the application of high-salinity molasses wastewater. After a stable start-up, methane production quickly decreased from 625 ± 17 to 232 ± 35 mL CH₄ L^-1 d^-1 with a simultaneous accumulation in volatile fatty acids up to 20.5 ± 1.4 g COD L^-1, indicating severe process disturbance. A shift in feedstock from molasses wastewater to waste activated sludge resulted in complete process recovery. However, the bacterial and archaeal communities did not return to their original composition as before the disturbance, despite similar process conditions. Microbial community diversity was recovered to similar levels as before disturbance, which indicates that the metabolic potential of the community was maintained. A mild increase in ammonia concentration after process recovery did not influence methane production, indicating a well-balanced microbial community. Hence, given the change in community composition following recovery after salinity disturbance, it can be assumed that microbial community redundancy was the major strategy to ensure the continuation of methane production, without loss of functionality or metabolic flexibility.

High-purity propionate production from glycerol in mixed culture fermentation

High-purity propionate production from glycerol in mixed culture fermentation (MCF) induced by high ammonium concentration was investigated. Fed-batch experiments revealed that higher ammonium concentration (>2.9g/L) had simultaneous negative effects on acetate and propionate degradation. Propionate production and yield was up to 22.6g/L and 0.45g COD/g COD glycerol, respectively, with a purity of 96%. Sequential batch experiments demonstrated that the yields of propionate were 0.3±0.05, 0.32±0.01, and 0.34±0.03g COD/g COD at a glycerol concentration of 2.78, 4.38, and 5.56g/L, respectively, and the purity of propionate was 91-100%. Microbial community analysis showed that the phylum Firmicutes dominated the bacterial community at different glycerol concentrations. However, the Methanosaeta population decreased from 46% to 6% when glycerol concentration increased from 2.78 to 5.56g/L, resulting in lower acetate degradation rate. Thus, the present study might provide an alternative option for the production of propionate from glycerol via MCF.