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.

Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics.

The presence of elevated ammonia levels is widely recognized as a significant contributor to process inhibition in biogas production, posing a common challenge for biogas plant operators. The present study employed a combination of biochemical, genome-centric metagenomic and metatranscriptomic data to investigate the response of the biogas microbiome to two shock loads induced by single pulses of elevated ammonia concentrations (i.e., 1.5 g NH4+/LR and 5 g NH4+/LR). The analysis revealed a microbial community of high complexity consisting of 364 Metagenome Assembled Genomes (MAGs). The hydrogenotrophic pathway was the primary route for methane production during the entire experiment, confirming its efficiency even at high ammonia concentrations. Additionally, metatranscriptomic analysis uncovered a metabolic shift in the methanogens Methanothrix sp. MA6 and Methanosarcina flavescens MX5, which switched their metabolism from the acetoclastic to the CO2 reduction route during the second shock. Furthermore, multiple genes associated with mechanisms for maintaining osmotic balance in the cell were upregulated, emphasizing the critical role of osmoprotection in the rapid response to the presence of ammonia. Finally, this study offers insights into the transcriptional response of an anaerobic digestion community, specifically focusing on the mechanisms involved in recovering from ammonia-induced stress.

DNA Metabarcoding from Microbial Communities Recovered from Stream and Its Potential for Bioremediation Processes.

Urban waste (UW) has caused a series of problems regarding its management. UW comprises domestic, hospital and industrial residues, which makes the destination of this waste a matter of concern, as it may contain a variety of highly toxic environmental polluters. Deactivated dumps can represent sources of contamination of the environment that surround these deposits, harming rivers and inhabiting organisms. Knowledge of the microbial profile of water bodies that can be affected by these toxic residues is essential for the development of alternatives and improvements in treatments applied in rivers and streams. In this sense, this work aimed to analyze the microbial community present in sediments of the Arroio Dourado stream in the municipality of Foz do Iguaçu, a stream located near a deactivated open-air dump. 16S rDNA metabarcoding suggested the dominance of acidogenic bacteria belonging to Acidobacteriota phylum, followed by less abundant phyla Actinobacteriota, Myxococcota, Chloroflexi and a small community of sulfate reducers (Desulfobacteriota). However, more than 50% of amplicon sequence variants (ASVs) were not taxonomically classified. In addition, an expressive abundance was attributed to the genus Anaeromyxobacter, a metabolically versatile group, which can thrive in the presence of polluting compounds present in the deactivated landfill. Thus, a possible stream treatment process can be developed. In addition, culture media can be developed for the recovery of taxonomic groups identified involved in the biodegradation of organic compounds. The results presented expand the knowledge of bacterial diversity in sediment samples recovered from the Arroio Dourado stream.

New Insights into Controlling Homoacetogenesis in the Co-digestion of Coffee Waste: Effect of Operational Conditions and Characterization of Microbial Communities.

In this research batch reactors were operated with coffee processing waste and autochthonous microbial consortium, and a taxonomic and functional analysis was performed for phase I of stabilization of maximum H2 production and for phase II of maximum H2 consumption. During phase I, the reactor's operating conditions were pH 4.84 to 8.18, headspace 33.18% to 66.82%, and pulp and husk from 6.95 to 17.05 g/L. These assays continued for phase II, with initial pH conditions of 5.8-8.1, headspace of 33.18-66.82%, and pulp and husk remaining from phase I. The highest homoacetogenesis was observed in assay 5 with pH 7.7, 40% headspace, and 15 g/L of pulp and husk (initial concentrations of phase I). A relative abundance of Clostridium 41%, Lactobacillus 20% and Acetobacter 14% was observed in phase I. In phase II, there was a change in relative abundance of 21%, 63%, and 1%, respectively, and functional genes involved with autotrophic (formyltetrahydrofolate synthase) and heterotrophic (enolase) homoacetogenesis, butanol (3-hydroxybutyryl-CoA dehydrogenase), and propionic acid (propionate CoA-transferase) were identified. This study provides a new and amplified insight into the physicochemical and microbiological factors, which can be used to propose adequate operational conditions to maximize the bioenergy production and reduce homoacetogenesis in biological reactors.