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

Multivariate comparison of taxonomic, chemical and operational data from 80 different full-scale anaerobic digester-related systems

BACKGROUND

The holistic characterization of different microbiomes in anaerobic digestion (AD) systems can contribute to a better understanding of these systems and provide starting points for bioengineering. The present study investigates the microbiome of 80 European full-scale AD systems. Operational, chemical and taxonomic data were thoroughly collected, analysed and correlated to identify the main drivers of AD processes.

RESULTS

The present study describes chemical and operational parameters for a broad spectrum of different AD systems. With this data, Spearman correlation and differential abundance analyses were applied to narrow down the role of the individual microorganisms detected. The authors succeeded in further limiting the number of microorganisms in the core microbiome for a broad range of AD systems. Based on 16S rRNA gene amplicon sequencing, MBA03, Proteiniphilum, a member of the family Dethiobacteraceae, the genus Caldicoprobacter and the methanogen Methanosarcina were the most prevalent and abundant organisms identified in all digesters analysed. High ratios for Methanoculleus are often described for agricultural co-digesters. Therefore, it is remarkable that Methanosarcina was surprisingly high in several digesters reaching ratios up to 47.2%. The various statistical analyses revealed that the microorganisms grouped according to different patterns. A purely taxonomic correlation enabled a distinction between an acetoclastic cluster and a hydrogenotrophic one. However, in the multivariate analysis with chemical parameters, the main clusters corresponded to hydrolytic and acidogenic microorganisms, with SAOB bacteria being particularly important in the second group. Including operational parameters resulted in digester-type specific grouping of microbes. Those with separate acidification stood out among the many reactor types due to their unexpected behaviour. Despite maximizing the organic loading rate in the hydrolytic pretreatments, these stages turned into extremely robust methane production units.

CONCLUSIONS

From 80 different AD systems, one of the most holistic data sets is provided. A very distinct formation of microbial clusters was discovered, depending on whether taxonomic, chemical or operational parameters were combined. The microorganisms in the individual clusters were strongly dependent on the respective reference parameters.

Microbial Diversity and Community Structure of Wastewater-Driven Microalgal Biofilms

Dwindling water sources increase the need for efficient wastewater treatment. Solar-driven algal turf scrubber (ATS) system may remediate wastewater by supporting the development and growth of periphytic microbiomes that function and interact in a highly dynamic manner through symbiotic interactions. Using ITS and 16S rRNA gene amplicon sequencing, we profiled the microbial communities of four microbial biofilms from ATS systems operated with municipal wastewater (mWW), diluted cattle and pig manure (CattleM and PigM), and biogas plant effluent supernatant (BGE) in comparison to the initial inocula and the respective wastewater substrates. The wastewater-driven biofilms differed significantly in their biodiversity and structure, exhibiting an inocula-independent but substrate-dependent establishment of the microbial communities. The prokaryotic communities were comparable among themselves and with other microbiomes of aquatic environments and were dominated by metabolically flexible prokaryotes such as nitrifiers, polyphosphate-accumulating and algicide-producing microorganisms, and anoxygenic photoautotrophs. Striking differences occurred in eukaryotic communities: While the mWW biofilm was characterized by high biodiversity and many filamentous (benthic) microalgae, the agricultural wastewater-fed biofilms consisted of less diverse communities with few benthic taxa mainly inhabited by unicellular chlorophytes and saprophytes/parasites. This study advances our understanding of the microbiome structure and function within the ATS-based wastewater treatment process.

Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes

Wastewater treatment plants (WWTPs) have been reported as major anthropogenic reservoirs for the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment, worldwide. While most studies mainly focus on the intracellular DNA (iDNA), extracellular DNA (exDNA) accounting for a significant proportion of the total DNA in wastewater, was usually neglected. Following the One Health approach, this study focuses on wastewaters of municipal, clinical, and livestock origins (n = 45) that undergo different treatment processes (i.e., conventional activated sludge, ultrafiltration, and ozonation). Water samples were analysed for 12 ARGs as indicators of the different compartments associated with iDNA and exDNA by quantitative real-time PCR (qPCR). Taxonomic profiling of exDNA-fractions, obtained using nucleic acid adsorption particles, was conducted by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Notified exDNA concentrations varied between on-site WWTPs and treatment stages, and ranged from 314.0 ± 70.2 ng/mL in untreated livestock wastewater down to 0.7 ± 0.1 ng/mL in effluents after ultrafiltration. In general, influents exhibited higher concentrations compared to effluents, while wastewater treated by advanced treatment processes (i.e., ultrafiltration and ozonation) showed the lowest exDNA concentrations. Despite the lower concentrations, free-floating exDNA accounted for up to 80.0 ± 5.8% of the total DNA in effluents. Target ARGs were more common in the iDNA (100%, n = 45/45), compared to the exDNA-fractions (51.1%, n = 23/45), whereas exDNA-ARGs were mostly detected in clinical and slaughterhouse wastewaters as well as in the municipal influents. Compared to the iDNA-ARGs, the concentrations of exDNA-ARGs were in general lower. Nevertheless, significant higher concentrations for exDNA-associated genes were measured in clinical wastewaters for blaNDM (4.07 ± 0.15 log gene copies (GC)/L) and blaVIM-2 (6.0 ± 0.2 log GC/L). Overall, our results suggest that depending on the origin of wastewater and its treatment methods, exDNA represents an important reservoir for ARGs, particularly in clinical wastewater.

Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics

The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.

Quantification of indicator and pathogenic bacteria in manures and digestates from three agricultural biogas plants over a one-year period

Interest in the conversion of manure in biogas via anaerobic digestion (AD) is growing, but questions remain about the biosafety of digestates. For a period of one year, we monitored the impact of three mesophilic agricultural biogas plants (BPs) mainly fed with pig manure (BP1, BP3) or bovine manure (BP2) on the physicochemical parameters, the composition of the microbial community and the concentration of bacteria (E. coli, enterococci, Salmonella, Campylobacter, Listeria monocytogenes, Clostridium perfringens, Clostridium botulinum and Clostridioides difficile). The BP2 digestate differed from those of the two other BPs with a higher nitrogen content, more total solids and greater abundance of Clostridia MBA03 and Disgonomonadacea. Persistence during digestion ranked from least to most, was: Campylobacter (1.6 to >2.9 log10 reduction, according to the BP) < E. coli (1.8 to 2.2 log10) < Salmonella (1.1 to 1.4 log10) < enterococci (0.2 to 1.2 log10) and C. perfringens (0.2 to 1 log10) < L. monocytogenes (-1.2 to 1.6 log10) < C. difficile and C. botulinum (≤0.5 log10). No statistical link was found between the reduction in the concentration of the targeted bacteria and the physicochemical and operational parameters likely to have an effect (NH3, volatile fatty acids and total solids contents, hydraulic retention time, presence of co-substrates), underlining the fact that the fate of the bacteria during mesophilic digestion depends on many interacting factors. The reduction in concentrations varied significantly over the sampling period, underlining the need for longitudinal studies to estimate the impact of AD on pathogenic microorganisms.

Controls on diversity of core and indicative microbial subcommunities in Tibetan Plateau grassland soils

Core subcommunity represents the less diversity but high abundance, while indicative subcommunity is highly diverse but low abundance in soils. The core subcommunity fundamentally maintains ecosystem stability, while the indicative plays important roles in vital ecosystem functions and is more sensitive to environmental change. However, their environmental driving factors and responses to human disturbances remain less defined. Herein, we explored the patterns of core and indicative soil microbes and their responses to animal grazing in dry grasslands across the Tibetan Plateau, using the Illumina sequencing of 16S rRNA gene. The results revealed that the core subcommunity diversity and richness were lower than the indicative in soils. The indicative subcommunity diversity exhibited substantially stronger correlations with nutrient-associated factors than the core diversity, including soil organic carbon, nitrogen, and plant biomass. The core and indicative microbial subcommunities both strongly varied with grassland ecosystems, while the latter was also significantly influenced by grazing. The variation partitioning analysis revealed that indicative microbial subcommunity was explained less by environmental factors than core subcommunity (34.5% vs 73.0%), but more influenced by grazing (2.6% vs 0.1%). Our findings demonstrated that the indicative microbes were particularly sensitive to soil nutrient-associated factors and human disturbances in alpine dry grasslands.

Effect of two-week red beetroot juice consumption on modulation of gut microbiota in healthy human volunteers - A pilot study

With very little research exploring intestinal effects of red beetroot consumption, the present pilot study investigated gut microbial changes following red beetroot consumption, via a 14-day intervention trial in healthy adults. Compared to baseline, the study demonstrates transient changes in abundance of some taxa e.g., Romboutsia and Christensenella, after different days of intervention (p < 0.05). Enrichment of Akkermansia muciniphila and decrease of Bacteroides fragilis (p < 0.05) were observed after 3 days of juice consumption, followed by restoration in abundance after 14 days. With native betacyanins and catabolites detected in stool after juice consumption, betacyanins were found to correlate positively with Bifidobacterium and Coprococcus, and inversely with Ruminococcus (p < 0.1), potentiating a significant rise in (iso)butyric acid content (172.7 ± 30.9 µmol/g stool). Study findings indicate the potential of red beetroot to influence gut microbial populations and catabolites associated with these changes, emphasizing the potential benefit of red beetroot on intestinal as well as systemic health.

The effect of substituting energy crop with agricultural waste on the dynamics of bacterial communities in a two-stage anaerobic digester

The replacement of energy crops with agricultural waste in biogas production through anaerobic digestion (AD) is both an environmentally sustainable and economically profitable strategy. However, the change of feeding mix in AD might result in nutrient imbalance or increase of the ammonium concentration, negatively affecting the activity of the microbes responsible for the process. In the present study the structure and dynamics of the bacterial communities of a full-scale two-stage AD plant, composed of a hydrolysis/acidogenesis (H) and an acetogenesis/methanogenesis (M) tanks, was monitored during feedstock substitution. Energy crop (triticale) was replaced by poultry manure litter and olive mill pomace. The increase percentage of poultry manure litter (up to 8.6%) and olive mill pomace (up to 30.5%) in the recipe incremented the total solids (up to 21% in H) and, consequently, the nitrogen content in the digestate (6.7 g N/kg in the solid fraction in H and 4-5 g NH₄⁺-N/L in the liquid fraction). This favored the growth of Lactococcus sp. with consequent increment of lactate production (∼ 1 mg L^-1 last two days of the survey) and the establishment of Weissella and Lactobacillus spp. Syntrophic acetate-oxidizers, including Syntrophaceticus (6% ± 1.7%), were detected manly in M but were negatively affected by the addition of the poultry manure litter, while the sulfate-reducing bacteria correlated with the variations of the volatile fatty acids. Planctomycetes putatively capable of anammox process were also found in the H during the first two days of the survey and accounted for 0.3 ± 0.01% of the total bacterial community. The stability of the process during feedstock change is the result of the shift of bacterial populations of different functional groups that showed peculiar adaptation patterns in the two stages of the plant.

Convergent Microbial Community Formation in Replicate Anaerobic Reactors Inoculated from Different Sources and Treating Ersatz Crew Waste

Future manned space travel will require efficient recycling of nutrients from organic waste back into food production. Microbial systems are a low-energy, efficient means of nutrient recycling, but their use in a life support system requires predictability and reproducibility in community formation and reactor performance. To assess the reproducibility of microbial community formation in fixed-film reactors, we inoculated replicate anaerobic reactors from two methanogenic inocula: a lab-scale fixed-film, plug-flow anaerobic reactor and an acidic transitional fen. Reactors were operated under identical conditions, and we assessed reactor performance and used 16s rDNA amplicon sequencing to determine microbial community formation. Reactor microbial communities were dominated by similar groups, but differences in community membership persisted in reactors inoculated from different sources. Reactor performance overlapped, suggesting a convergence of both reactor communities and organic matter mineralization. The results of this study suggest an optimized microbial community could be preserved and used to start new, or restart failed, anaerobic reactors in a life support system with predictable reactor performance.