Thermophilic anaerobic degradation of carbohydrates - metabolic properties of microorganisms from the different phases

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes

BACKGROUND

The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production.

RESULTS

The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs.

CONCLUSIONS

This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.

Effect of temperature increase from 55 to 65 degrees C on performance and microbial population dynamics of an anaerobic reactor treating cattle manure

The effect of a temperature increase from 55 to 65 degrees C on process performance and microbial population dynamics were investigated in thermophilic, lab-scale, continuously stirred tank reactors. The reactors had a working volume of 31 and were fed with cattle manure at an organic loading rate of 3 g VS/l reactor volume/d. The hydraulic retention time in the reactors was 15 days. A stable reactor performance was obtained for periods of three retention times both at 55 degrees C and 65 degrees C. At 65 degrees C methane yield stabilized at approximately 165ml/g VS/d compared to 200 ml/g VS/d at 55 degrees C. Simultaneously, the level of total volatile fatty acids, VFA, increased from being below 0.3 g/l to 1.8-2.4 g acetate/l. The specific methanogenic activities (SMA) of biomass from the reactors were measured with acetate, propionate, butyrate, hydrogen, formate and glucose. At 65 degrees C. a decreased activity was found for glucose-, acetate-, butyrate- and formate-utilizers and no significant activity was measured with propionate. Only the hydrogen-consuming methanogens showed an enhanced activity at 65 degrees C. Numbers of cultivable methanogens, estimated by the most probable number (MPN) method, were significantly lower on glucose, acetate and butyrate at the increased operational temperature, while the numbers of hydrogenotrophic methanogens remained unchanged. No viable propionate-degrading bacteria were enriched at 65 C. Use of ribosomal oligonucleotide probes showed that an increase in temperature resulted in a decreased contribution of the rRNA of the domain bacteria from 74-79 to 57-62% of the universal probe, while the rRNA of the domain archaea, increased from 18-23 to 34-36%.

Thermozymes

Enzymes synthesized by thermophiles (organisms with optimal growth temperatures > 60 degrees C) and hyperthermophiles (optimal growth temperatures > 80 degrees C) are typically thermostable (resistant to irreversible inactivation at high temperatures) and thermophilic (optimally active at high temperatures, i.e., > 60 degrees C). These enzymes, called thermozymes, share catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, thermozymes usually retain their thermal properties, suggesting that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, and crystal structure comparisons indicate that thermozymes are, indeed, very similar to mesophilic enzymes. No obvious sequence or structural features account for enzyme thermostability and thermophilicity. Thermostability and thermophilicity molecular mechanisms are varied, differing from enzyme to enzyme. Thermostability and thermophilicity are usually caused by the accumulation of numerous subtle sequence differences. This review concentrates on the mechanisms involved in enzyme thermostability and thermophilicity. Their relationships with protein rigidity and flexibility and with protein folding and unfolding are discussed. Intrinsic stabilizing forces (e.g., salt bridges, hydrogen bonds, hydrophobic interactions) and extrinsic stabilizing factors are examined. Finally, thermozymes' potential as catalysts for industrial processes and specialty uses are discussed, and lines of development (through new applications, and protein engineering) are also proposed.

Glucose catabolism by Spirochaeta thermophila RI 19.B1

Spirochaeta thermophila RI 19.B1 (DSM 6192) fermented glucose to lactate, acetate, CO2, and H2 with concomitant formation of cell material. The cell dry mass yield was 20.0 g/mol of glucose. From the fermentation balance data and knowledge of the fermentation pathway, a YATP of 9.22 g of dry mass per mol of ATP was calculated for pH-uncontrolled batch-culture growth on glucose in a mineral medium. Measurement of enzyme activities in glucose-grown cells revealed that glucose was taken up by a permease and then subjected to ATP-dependent phosphorylation by a hexokinase. Glucose-6-phosphate was further metabolized to pyruvate through the Embden-Meyerhof-Parnas pathway. The phosphoryl donor for phosphofructokinase activity was PPi rather than ATP. This was also found for the type strain of S. thermophila, Z-1203 (DSM 6578). PPi was probably formed by pyrophosphoroclastic cleavage of ATP, with recovery of the resultant AMP by the activity of adenylate kinase. All other measured kinase activities utilized ATP as the phosphoryl donor. Pyruvate was further metabolized to acetyl coenzyme A with concomitant production of H2 and CO2 by pyruvate synthase. Lactate was also produced from pyruvate by a fructose-1,6-diphosphate-insensitive lactate dehydrogenase. Evidence was obtained for the transfer of reducing equivalents from the glycolytic pathway to hydrogenase to produce H2. No formate dehydrogenase or significant ethanol-producing enzyme activities were detected.