@misc{OttoPucholRoyoOrtegaLegarretaetal., author = {Otto, Pascal and Puchol-Royo, Roser and Ortega-Legarreta, Asier and Tanner, Kristie and Tideman, Jeroen and De Vries, Sjoerd-Jan and Pascual, Javier and Porcar, Manuel and Latorre-P{\´e}rez, Adriel and Abendroth, Christian}, title = {Multivariate comparison of taxonomic, chemical and operational data from 80 different full-scale anaerobic digester-related systems}, series = {Biotechnology for Biofuels and Bioproducts}, volume = {17}, journal = {Biotechnology for Biofuels and Bioproducts}, doi = {10.1186/s13068-024-02525-1}, pages = {1 -- 17}, abstract = {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.}, language = {en} } @misc{VidalVerduTorrentIglesiasetal., author = {Vidal-Verd{\´u}, {\`A}ngela and Torrent, Daniel and Iglesias, Alba and Latorre-P{\´e}rez, Adriel and Abendroth, Christian and Corb{\´i}n-Agust{\´i}, Paola and Peret{\´o}, Juli and Porcar, Manuel}, title = {The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications}, series = {npj Biofilms and Microbiomes}, volume = {10}, journal = {npj Biofilms and Microbiomes}, number = {1}, publisher = {Springer Science and Business Media LLC}, issn = {2055-5008}, doi = {10.1038/s41522-024-00531-7}, pages = {14}, abstract = {Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.}, language = {en} } @misc{Puchol‐RoyoPascualOrtega‐Legarretaetal., author = {Puchol-Royo, Roser and Pascual, Javier and Ortega-Legarreta, Asier and Otto, Pascal and Tideman, Jeroen and de Vries, Sjoerd-Jan and Abendroth, Christian and Tanner, Kristie and Porcar, Manuel and Latorre-Perez, Adriel}, title = {Metagenomic insights into the ecology, taxonomy and metabolic capabilities of 'Candidatus Darwinibacteriales' Ord. Nov. (formerly MBA03), a potential key player in anaerobic digestionstion}, series = {Microbial biotechnology}, volume = {18}, journal = {Microbial biotechnology}, number = {12}, publisher = {Wiley}, address = {Hoboken, NJ}, issn = {1751-7915}, doi = {10.1111/1751-7915.70258}, pages = {1 -- 16}, abstract = {Biogas, a mix of CO2, CH4 and small proportions of other gases, is a biofuel obtained by anaerobic digestion (AD). Biogas production is often considered a black box process, as the role and dynamics of some of the microorganisms involved remain undisclosed. Previous metataxonomic studies in the frame of the MICRO4BIOGAS project (www. micro 4biog as. eu) revealed that MBA03, an uncharacterised and uncultured bacterial taxon belonging to phylum Bacillota, was very prevalent and abundant in industrial full-scale AD plants. Despite the efforts, this taxon has not yet been cultivated, which makes the analysis of its taxonomy, ecology and metabolism even more challenging. In the present work, 30 samples derived from anaerobic digesters were sequenced, allowing the reconstruction of 108 metagenome-assembled genomes (MAGs) potentially belonging to MBA03. According to phylogenetic analyses and genomic similarity indices, MBA03 was classified as a new bacterial order, proposed as 'Candidatus Darwinibacteriales' ord. nov., which includes 'Candidatus Darwinibacter acetoxidans' gen. nov., sp. nov. of 'Candidatus Darwinibacteriaceae' fam. nov., along with 'Candidatus Wallacebacter cryptica' gen. nov., sp. nov. of the 'Candidatus Wallacebacteriaceae' fam. nov. Ecotaxonomic studies determined that AD processes are the main ecological niche of 'Candidatus Darwinibacteriales'. Moreover, metabolic predictions identified Darwinibacteraceae members as putative syntrophic acetate-oxidising bacteria (SAOB), as they encode for the reversed Wood-Ljungdahl (W-L) pathway coupled to the glycine cleavage system. This suggests that Darwinibacteraceae members could work in collaboration with hydrogenotrophic methanogenic archaea to produce methane in industrial biogas plants. Overall, our findings present 'Candidatus Darwinibacteriales' as a potential key player in anaerobic digestion and pave the way towards the complete characterisation of this newly described bacterial taxon, which has not yet been cultured.}, language = {en} }