Biology subjects

Angelidaki, I.

Publications and source records attributed to Angelidaki, I..

4 recordsLinked to original sources

bioRxiv2026

Increased substrate complexity drives re-diversification and functional reorganization in simplified methanogenic consortia

Anaerobic digestion is a sustainable process for methane production that relies on complex microbial networks. While simplified enriched consortia offer a promising strategy to improve process control, excessive simplification can disrupt key functions and microbial partnerships, reducing community resilience. In this study, we investigated whether simplified methanogenic communities could re-diversify and maintain methane production when exposed to more complex substrates, namely butyrate and glucose. We also evaluated the effect of vitamin and amino acid supplementation on sustaining key methanogens and beneficial microbial partners. Three methanogenic communities were monitored over three months for methane production and microbial diversity while receiving butyrate and/or glucose, with different vitamin or amino acid supplements. Exposure to more complex substrates successfully restored the diversity of acidogenic and acetogenic populations, even after prolonged feeding with simple substrates, highlighting both the resilience of the simplified communities and the ecological importance of low-abundance taxa. However, the transition reduced process stability and methane production, likely due to substrate overloading. The results further suggest that substrate complexification should be introduced stepwise, promoting acetogenesis before acidogenesis. This fundamental study brings new light on which factors must be considered in the long-term goal of designing tailored-made consortia for anaerobic digestion.

bioengineering↗

bioRxiv2025

Beyond magnetosomes: ubiquitous and diverse intracellular inclusions expand the role of magnetotactic bacteria in biogeochemical cycling

Magnetotactic bacteria (MTB) are capable of accumulating and storing intercellular pools containing phosphorus, sulfur, nitrogen and carbon. Yet, the metabolic pathways connected with their intracellular storage of polyphosphate, elemental sulfur, nitrate, and calcium carbonate, and the environmental influence on MTB inclusions and their quantitative contribution to sedimentary chemical budgets remain underexplored. Using a combination of chemical characterization, ultrastructural and compositional analyses, and phylogenetic and genomic insights into microbial assemblages, we investigated the influence of geochemical parameters on the diversity, ecophysiology, and distribution of MTB in freshwater and brackish sediments. Special focus is given to intracellular inclusions and their metabolic pathways to uncover functional traits and ecological roles in elemental cycling. Of the 118 examined MTB cells, polyphosphate granules (75%) and nitrate-containing vacuoles (67%) were the most common inclusions followed by sulfur globules (25%) and calcium carbonate granules (8%). The intracellular phosphorus, nitrogen, and sulfur stored in MTB cells were conservatively estimated to account for 0.60%, 0.91%, and 0.23% of the total sedimentary P, N, and S in the investigated freshwater sediments, respectively. The ubiquitous nature and important ecological role of MTB can be explained by their ability to sequester chemical elements into intracellular inclusions, giving them a metabolic advantage in dynamic chemically stratified environments. The extraordinary phylogenetic diversity of MTB, coupled with their capability to hyperaccumulate and store a wide range of elements and compounds, represents a significant resource for biotechnology innovation.

microbiology↗

bioRxiv2019

The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production

BackgroundMicroorganisms in biogas reactors are essential for degradation of organic matter and methane production through anaerobic digestion process. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository.\n\nResultsHere, 134 publicly available datasets derived from different biogas reactors were used to recover 1,635 metagenome-assembled genomes (MAGs) representing different bacterial and archaeal species. All genomes were estimated to be >50% complete and nearly half were [≥]90% complete with [≤]5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth rate for microbes involved in different steps of the food chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter.\n\nConclusionsThe outcome of this study highlights a high flexibility of the biogas microbiome. The dynamic composition and adaptability to the environmental conditions, including temperatures and a wide range of substrates, were demonstrated. Our findings enhance the mechanistic understanding of anaerobic digestion microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.

microbiology↗

bioRxiv2018

Genome-centric metagenomics revealed the spatial distribution and the diverse metabolic functions of lignocellulose degrading uncultured bacteria

The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material allowing them to efficiently decompose the organic matter are far to be elucidated. To circumvent this issue, the microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads followed by binning process recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution into the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes can vary depending on the number and functional roles of carbohydrate-binding modules. On contrary, members of Bacteroidetes are able to adhere and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics allowing a functional and taxonomical exploration of the biogas microbiome.\n\nImportanceThis work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales. Even though structural elements of cellulosome were restricted to Clostridiales, our study identified in Bacteroidetes a putative mechanism for biomass decomposition based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose and transport to cytoplasm.

microbiology↗