23 results on '"Panagiotis S. Adam"'
Search Results
2. Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core
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Yunha Hwang, Dirk Schulze-Makuch, Felix L. Arens, Johan S. Saenz, Panagiotis S. Adam, Christof Sager, Till L. V. Bornemann, Weishu Zhao, Ying Zhang, Alessandro Airo, Michael Schloter, and Alexander J. Probst
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Atacama ,Hyperaridity ,Archaea ,Soil microbiome ,Xerotolerance ,Microbial ecology ,QR100-130 - Abstract
Abstract Background The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core. Results Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Conclusion We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract
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- 2021
- Full Text
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3. Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities
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Perla Abigail Figueroa-Gonzalez, Till L. V. Bornemann, Panagiotis S. Adam, Julia Plewka, Fruzsina Révész, Christian A. von Hagen, András Táncsics, and Alexander J. Probst
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hydrocarbon degradation ,symbionts ,groundwater ,genome-resolved metagenomics ,enrichment cultures ,Microbiology ,QR1-502 - Abstract
Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.
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- 2020
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4. Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes
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Benjamin H Meyer, Panagiotis S Adam, Ben A Wagstaff, George E Kolyfetis, Alexander J Probst, Sonja V Albers, and Helge C Dorfmueller
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Sulfolobus acidocladarius ,N-glycosylation ,chitobiose ,Agl24 ,Alg13 ,Alg14 ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.
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- 2022
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5. Progress and Challenges in Studying the Ecophysiology of Archaea
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Panagiotis S, Adam, Till L V, Bornemann, and Alexander J, Probst
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Genome, Archaeal ,Alkanes ,Archaea ,Methane ,Phylogeny - Abstract
It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.
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- 2022
6. Reconstruction of Archaeal Genomes from Short-Read Metagenomes
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Till L V, Bornemann, Panagiotis S, Adam, and Alexander J, Probst
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Genome, Archaeal ,Nucleic Acids ,Metagenome ,RNA ,Lipids - Abstract
As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in particular suffer from a multitude of issues that make their culturing problematic, from them being frequently members of the rare biosphere, to low growth rates, to them thriving under very specific and often extreme environmental and community conditions that are difficult to replicate. OMICs techniques are state of the art approaches that allow direct high-throughput investigations of environmental samples at all levels from nucleic acids to proteins, lipids, and secondary metabolites. Metagenomics, as the foundation for other OMICs techniques, facilitates the identification and functional characterization of the microbial community members and can be combined with other methods to provide insights into the microbial activities, both on the RNA and protein levels. In this chapter, we provide a step-by-step workflow for the recovery of archaeal genomes from metagenomes, starting from raw short-read sequences. This workflow can be applied to recover bacterial genomes as well.
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- 2022
7. Author response: Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes
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Benjamin H Meyer, Panagiotis S Adam, Ben A Wagstaff, George E Kolyfetis, Alexander J Probst, Sonja V Albers, and Helge C Dorfmueller
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- 2022
8. Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling
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Panagiotis S. Adam, George E. Kolyfetis, Till L. V. Bornemann, Constantinos E. Vorgias, and Alexander J. Probst
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Multidisciplinary ,Chemie - Abstract
Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO 2 -reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called “methanogenesis markers” but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.
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- 2022
9. Reconstruction of Archaeal Genomes from Short-Read Metagenomes
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Till L. V. Bornemann, Panagiotis S. Adam, and Alexander J. Probst
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Chemie ,Biologie - Published
- 2022
10. Progress and Challenges in Studying the Ecophysiology of Archaea
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Panagiotis S. Adam, Till L. V. Bornemann, and Alexander J. Probst
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Chemie - Published
- 2022
11. Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling
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Panagiotis S. Adam, Constantinos E. Vorgias, Till L. V. Bornemann, George E. Kolyfetis, and Alexander J. Probst
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Genetics ,chemistry.chemical_compound ,Hydrogenase ,biology ,chemistry ,Methanogenesis ,Autotroph ,biology.organism_classification ,Anoxic waters ,Gene ,Methanogen ,Methane ,Archaea - Abstract
Methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Other than its two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), there exist other genes called “methanogenesis markers” that are believed to participate in methane metabolism. Many of them are Domains of Unknown Function. Here we show that these markers emerged together with methanogenesis. Even if Mcr is lost, the markers and Mtr can persist resulting in intermediate metabolic states related to the Wood-Ljungdahl pathway. Beyond the markers, the methanogenic ancestor was hydrogenotrophic, employing the anaplerotic hydrogenases Eha and Ehb. The selective pressures acting on Eha, Ehb, and Mtr partially depend on their subunits’ membrane association. Integrating the evolution of all these components, we propose that the ancestor of all methane metabolizers was an autotrophic H2/CO2 methanogen that could perhaps use methanol but not oxidize alkanes. Hydrogen-dependent methylotrophic methanogenesis has since emerged multiple times independently, both alongside a vertically inherited Mcr or from a patchwork of ancient transfers. Through their methanogenesis genomic remnants, Thorarchaeota and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeota act as metabolically versatile players in carbon cycling of anoxic environments across the globe.
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- 2021
12. N-glycan chitobiose core biosynthesis by Agl24 strengthens the hypothesis of an archaeal origin of the eukaryal N-glycosylation
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Ben A. Wagstaff, Benjamin H. Meyer, Helge C. Dorfmueller, Panagiotis S. Adam, and Sonja-Verena Albers
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Glycan ,Glycosylation ,biology ,Chitobiose ,biology.organism_classification ,chemistry.chemical_compound ,N-linked glycosylation ,Biochemistry ,chemistry ,Glycosyltransferase ,biology.protein ,Histidine ,Function (biology) ,Archaea - Abstract
Protein N-glycosylation is the most common posttranslational modifications found in all three domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in eukaryotes. Here, we report the identification of a thermostable archaeal beta-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed the function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed strong similarities between Agl24 and both the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which catalyze the identical or a similar process, respectively. Our data, complemented by phylogenetic analysis of Alg13 and Alg14, revealed similar sequences in Asgardarchaeota, further supporting the hypothesis that the Alg13/14 homologs in eukaryotes have been acquired during eukaryogenesis.HighlightsFirst identification and characterization of a thermostable β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase (GT family 28) in Archaea.A highly conserved histidine, within a GGH motif in Agl24, Alg14, and MurG, is essential for function of Agl24.Agl24-like homologs are broadly distributed among Archaea.The eukaryotic Alg13 and Alg14 are closely related to the Asgard homologs, suggesting their acquisition during eukaryogenesis.
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- 2021
13. Leave no stone unturned : individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core
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Johan S. Saenz, Yunha Hwang, Dirk Schulze-Makuch, Weishu Zhao, Christof Sager, Ying Zhang, Felix L. Arens, Panagiotis S. Adam, Till L. V. Bornemann, Michael Schloter, Alessandro Airo, and Alexander J. Probst
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Microbiology (medical) ,Thaumarchaeota ,Lineage (evolution) ,Chemie ,Atacama ,Biology ,Microbiology ,Forschungszentren » Zentrum für Wasser- und Umweltforschung (ZWU) ,Microbial ecology ,ddc:570 ,Ecosystem ,Hyperaridity ,Soil Microbiology ,Soil microbiome ,Bacteria ,Ecology ,Research ,Microbiota ,QR100-130 ,biology.organism_classification ,Archaea ,Fakultät für Chemie » Umweltmikrobiologie und Biotechnologie (UMB) ,Habitat ,Metagenomics ,ddc:540 ,Candidatus ,Soil Microbiome ,Xerotolerance ,Desert Climate - Abstract
Background: The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core. Results: Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Conclusion: We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Conclusion: We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems.
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- 2021
14. Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition
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Jerzy Witwinowski, Simonetta Gribaldo, Guillaume Borrel, Panagiotis S. Adam, Daniela Megrian, Najwa Taib, Christophe Beloin, Daniel Poppleton, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Génétique des Biofilms - Genetics of Biofilms, S.G., C.B. and J.W. acknowledge funding from the French National Research Agency (ANR), project Fir-OM (grant no. ANR-16-CE12-0010) and from the Institut Pasteur Programmes Transversaux de Recherche (grant no. PTR 39–16). D.M. and D.P. were supported by the Pasteur-Paris University (PPU) International PhD Program. This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris., ANR-16-CE12-0010,Fir-OM,Firmicutes avec une membrane externe: vers des nouveaux modeles d'étude de la transition monodermes/didermes(2016), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Collège Doctoral
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Firmicutes ,Chemie ,Gram-Positive Bacteria ,Genome ,MESH: Gram-Positive Bacteria ,03 medical and health sciences ,Gram-Negative Bacteria ,MESH: Gram-Negative Bacteria ,Humans ,Clade ,MESH: Phylogeny ,MESH: Firmicutes ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,030304 developmental biology ,0303 health sciences ,Halanaerobiales ,Negativicutes ,MESH: Humans ,Ecology ,Phylogenetic tree ,biology ,Bacteria ,030306 microbiology ,Phylum ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,MESH: Bacteria ,Evolutionary biology ,Bacterial outer membrane - Abstract
Phylogenomic analysis supports a diderm ancestor of the Firmicutes and points to an early origin of two-membraned cells in Bacteria and the derived nature of the Gram-positive envelope following multiple outer membrane losses. The transition between cell envelopes with one membrane (Gram-positive or monoderm) and those with two membranes (Gram-negative or diderm) is a fundamental open question in the evolution of Bacteria. Evidence of the presence of two independent diderm lineages, the Halanaerobiales and the Negativicutes, within the classically monoderm Firmicutes has blurred the monoderm/diderm divide and specifically anticipated that other members with an outer membrane (OM) might exist in this phylum. Here, by screening 1,639 genomes of uncultured Firmicutes for signatures of an OM, we highlight a third and deep branching diderm clade, the Limnochordia, strengthening the hypothesis of a diderm ancestor and the occurrence of independent transitions leading to the monoderm phenotype. Phyletic patterns of over 176,000 protein families constituting the Firmicutes pan-proteome identify those that strongly correlate with the diderm phenotype and suggest the existence of new potential players in OM biogenesis. In contrast, we find practically no largely conserved core of monoderms, a fact possibly linked to different ways of adapting to repeated OM losses. Phylogenetic analysis of a concatenation of main OM components totalling nearly 2,000 amino acid positions illustrates the common origin and vertical evolution of most diderm bacterial envelopes. Finally, mapping the presence/absence of OM markers onto the tree of Bacteria shows the overwhelming presence of diderm phyla and the non-monophyly of monoderm ones, pointing to an early origin of two-membraned cells and the derived nature of the Gram-positive envelope following multiple OM losses.
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- 2020
15. Leave no stone unturned: The hidden potential of carbon and nitrogen cycling by novel, highly adapted Thaumarchaeota in the Atacama Desert hyperarid core
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Dirk Schulze-Makuch, Till L. V. Bornemann, Johan S. Saenz, Alessandro Airo, Michael Schloter, Panagiotis S. Adam, Felix L. Arens, Yunha Hwang, and Alexander J. Probst
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Comparative genomics ,Thaumarchaeota ,biology ,Ecology ,Carbon fixation ,Heterotroph ,Ecosystem ,Microbiome ,biology.organism_classification ,Genome ,Nitrogen cycle - Abstract
The hyperarid core of the Atacama Desert is an extremely harsh environment previously thought to be colonized by only a few heterotrophic bacterial species. In addition, carbon and nitrogen cycling in these highly oligotrophic ecosystems are poorly understood. Here we genomically resolved a novel genus of Thaumarchaeota, Ca. Nitrosodesertus, found below boulders of the Atacama hyperarid core, and used comparative genomics to analyze their pangenome and site-specific adaptations. Their genomes contain genes for ammonia oxidation and the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, indicating a chemolithoautotrophic lifestyle. Ca. Nitrosodesertus possesses the capacity for tolerating extensive environmental stress highlighted by the presence of genes against oxidative stress, DNA damage and genes for the formation of biofilms. These features are likely responsible for their dominance in samples with extremely low water content across three different boulder fields and eight different boulders. Genome-specific adaptations of the genomes included the presence of additional genes for UV resistance, heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Our results suggest that Thaumarchaeota mediate important carbon and nitrogen cycling in the hyperarid core of the Atacama and are part of its continuous and indigenous microbiome.
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- 2020
16. Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing
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Till L. V. Bornemann, Panagiotis S. Adam, Victoria Turzynski, Ulrich Schreiber, Perla Abigail Figueroa-Gonzalez, Janina Rahlff, Daniel Köster, Torsten C. Schmidt, Ralf Schunk, Bernhard Krauthausen, and Alexander J. Probst
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Water microbiology ,Multidisciplinary ,Bacteria ,Geography & travel ,Science ,Chemie ,General Physics and Astronomy ,Genetic Variation ,Geology ,General Chemistry ,Archaea ,General Biochemistry, Genetics and Molecular Biology ,Article ,Microbial ecology ,Prokaryotic Cells ,Metagenomics ,Biologie ,Ecosystem ,Phylogeny ,Soil Microbiology ,ddc:910 - Abstract
Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere., Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
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- 2020
17. Geological degassing enhances microbial metabolism in the continental subsurface
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Alexander J. Probst, Ulrich C. Schreiber, Victoria Turzynski, Panagiotis S. Adam, Torsten C. Schmidt, Till L. V. Bornemann, Perla Abigail Figueroa-Gonzalez, Daniel Koester, Bernhard Krauthausen, Janina Rahlff, and Ralf Schunk
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geography ,geography.geographical_feature_category ,Nutrient ,Volcano ,Metagenomics ,Earth science ,Microbial metabolism ,Environmental science ,Ecosystem ,Mantle (geology) ,Groundwater ,Bacterial replication - Abstract
Mantle degassing provides a substantial amount of reduced and oxidized gases shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we characterized deep subsurface fluids from a cold-water geyser driven by mantle degassing using genome-resolved metagenomics to investigate how the gases impact the metabolism and activity of indigenous microbes compared to non-impacted sites. While species-specific analyses of Altiarchaeota suggest site-specific adaptations and a particular biogeographic pattern, chemolithoautotrophic core features of the communities appeared to be conserved across 17 groundwater ecosystems between 5 and 3200 m depth. We identified a significant negative correlation between ecosystem depth and bacterial replication, except for samples impacted by high amounts of subsurface gases, which exhibited near-surface activity. Our results suggest that geological degassing leads to higher nutrient flows and microbial activity in the deep subsurface than previously estimated.
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- 2020
18. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology
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Guillaume Borrel, Céline Brochier-Armanet, Panagiotis S. Adam, Simonetta Gribaldo, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), PSA is supported by a PhD fellowship from Paris Diderot University and funds by the PhD Programme ‘Frontières du Vivant (FdV) – Programme Bettencourt’. GB is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. SG and CB-A acknowledge funding by the French National Agency for Research (ANR) grant ArchEvol (ANR-16-CE02-0005-01)., We thank the three anonymous reviewers for very useful comments and suggestions. Finally, we apologize to colleagues whose work could not be cited due to space limitations., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]
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MESH: Ecology ,0301 basic medicine ,MESH: Genome, Archaeal ,Mini Review ,MESH: Biodiversity ,[SDV]Life Sciences [q-bio] ,media_common.quotation_subject ,Ecology (disciplines) ,Tree of life (biology) ,Biodiversity ,Microbiology ,03 medical and health sciences ,Genome, Archaeal ,Phylogenetics ,MESH: Archaea/genetics ,MESH: Phylogeny ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,media_common ,Ecology ,biology ,Phylum ,MESH: Archaea/isolation & purification ,Human microbiome ,15. Life on land ,biology.organism_classification ,Archaea ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,030104 developmental biology ,13. Climate action ,MESH: Archaea/classification ,Diversity (politics) - Abstract
International audience; The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.
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- 2017
19. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea
- Author
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Panagiotis S. Adam, Guillaume Borrel, Wen-Jun Li, Steven J. Hallam, William P. Inskeep, Luke J. McKay, Gary L. Andersen, Simonetta Gribaldo, Quentin Letourneur, Amine Ghozlane, Isabel N. Sierra-Garcia, Gerard Muyzer, Valéria Maia de Oliveira, Lin-Xing Chen, Jillian F. Banfield, Christian M. K. Sieber, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), Montana State University (MSU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University [Guangzhou] (SYSU), University of British Columbia (UBC), University of Amsterdam [Amsterdam] (UvA), G.B. acknowledges support from the Institut Pasteur through a Roux-Cantarini fellowship. P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme ‘Frontières du Vivant (FdV)-Programme Bettencourt’. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (No. ANR-16-CE02-0005-01). This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris. S.J.H. acknowledges support from the US Department of Energy (DOE) JGI supported by the Office of Science of US DOE Contract No. DE-AC02–05CH11231, the Natural Sciences and Engineering Research Council (NSERC) of Canada, Genome British Columbia, Genome Canada, Canada Foundation for Innovation (CFI) and the Tula Foundation. I.N.S.-G. and V.M.d.O. are grateful to São Paulo Research Foundation—FAPESP (process Nos. 2011/14501-6 and 2013/20436-8) and Petrobras for financial support and to N. Gray and I. Head from the School of Civil Engineering and Geosciences at Newcastle University for lab facilities. W-J.L. was supported by Key Projects of Ministry of Science and Technology (MOST) (Nos. 2013DFA31980 and 2015FY110100). G.M. was supported by the ERC Advanced Grant PARASOL (No. 322551). L.J.M. appreciates funding from the NASA Postdoctoral Programme through the NASA Astrobiology Institute and W.P.I. was supported by the Montana Agricultural Experiment Station (Project No. 911300)., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), European Project: 322551,EC:FP7:ERC,ERC-2012-ADG_20120314,PARASOL(2013), Institut Pasteur [Paris], University of Campinas [Campinas] (UNICAMP), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University (SYSU), and Freshwater and Marine Ecology (IBED, FNWI)
- Subjects
Microbiology (medical) ,Methanogenesis ,Immunology ,Biodiversity ,Biology ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Applied Microbiology and Biotechnology ,Microbiology ,Genome ,Article ,03 medical and health sciences ,Phylogenetics ,Alkanes ,Genetics ,Gene ,Phylogeny ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,DNA ,Cell Biology ,biology.organism_classification ,Archaea ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Archaeal ,Medical Microbiology ,13. Climate action ,Metagenomics ,Evolutionary biology ,Candidatus ,Metagenome ,Methane ,Oxidation-Reduction - Abstract
International audience; Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.
- Published
- 2019
20. HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses
- Author
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Constantinos E. Vorgias, George Nounesis, Anna C. Papageorgiou, Rob Meijers, Philemon Stavros, Panagiotis S. Adam, and Kyriacos Petratos
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0301 basic medicine ,Hot Temperature ,Thermales ,Computational biology ,Microbiology ,DNA-binding protein ,Conserved sequence ,Evolution, Molecular ,03 medical and health sciences ,Bacterial Proteins ,Gene ,Conserved Sequence ,Thermostability ,Genetics ,030102 biochemistry & molecular biology ,biology ,Protein Stability ,Thermus thermophilus ,General Medicine ,Evolutionary pressure ,biology.organism_classification ,DNA-Binding Proteins ,030104 developmental biology ,Molecular Medicine ,Function (biology) ,Protein Binding - Abstract
The histone-like DNA-binding proteins (HU) serve as model molecules for protein thermostability studies, as they function in different bacteria that grow in a wide range of temperatures and show sequence diversity under a common fold. In this work, we report the cloning of the hutth gene from Thermus thermophilus, the purification and crystallization of the recombinant HUTth protein, as well as its X-ray structure determination at 1.7 Å. Detailed structural and thermodynamic analyses were performed towards the understanding of the thermostability mechanism. The interaction of HUTth protein with plasmid DNA in solution has been determined for the first time with MST. Sequence conservation of an exclusively thermophilic order like Thermales, when compared to a predominantly mesophilic order (Deinococcales), should be subject, to some extent, to thermostability-related evolutionary pressure. This hypothesis was used to guide our bioinformatics and evolutionary studies. We discuss the impact of thermostability adaptation on the structure of HU proteins, based on the detailed evolutionary analysis of the Deinococcus-Thermus phylum, where HUTth belongs. Furthermore, we propose a novel method of engineering thermostable proteins, by combining consensus-based design with ancestral sequence reconstruction. Finally, through the structure of HUTth, we are able to examine the validity of these predictions. Our approach represents a significant advancement, as it explores for the first time the potential of ancestral sequence reconstruction in the divergence between a thermophilic and a mainly mesophilic taxon, combined with consensus-based engineering.
- Published
- 2016
21. An archaeal origin of the Wood-Ljungdahl H
- Author
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Panagiotis S, Adam, Guillaume, Borrel, and Simonetta, Gribaldo
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Evolution, Molecular ,Bacteria ,Gene Transfer, Horizontal ,Genome, Archaeal ,Archaea ,Methane ,Wood ,Carbon ,Genome, Bacterial ,Phylogeny ,Genes, Archaeal ,Pterins - Abstract
The tetrahydromethanopterin (H
- Published
- 2018
22. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes
- Author
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Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]
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0301 basic medicine ,Enzyme complex ,MESH: Genome, Archaeal ,LUCA ,[SDV]Life Sciences [q-bio] ,MESH: Genome, Bacterial ,Genome ,Corrections ,chemistry.chemical_compound ,Genome, Archaeal ,MESH: Multienzyme Complexes/genetics ,methanogens ,Phylogeny ,MESH: Phylogeny ,Genetics ,Carbon Monoxide ,Multidisciplinary ,Last universal ancestor ,Carbon fixation ,Acetyl-CoA ,MESH: Carbon Cycle ,Aldehyde Oxidoreductases ,Biological Evolution ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,PNAS Plus ,MESH: Bacteria/enzymology ,Wood–Ljungdahl pathway ,Wood-Ljungdahl pathway ,MESH: Aldehyde Oxidoreductases/metabolism ,Carbon monoxide dehydrogenase ,030106 microbiology ,MESH: Bacteria/genetics ,Acetate-CoA Ligase ,Bacterial genome size ,Biology ,MESH: Biological Evolution ,MESH: Aldehyde Oxidoreductases/genetics ,Carbon Cycle ,03 medical and health sciences ,MESH: Carbon Monoxide/metabolism ,Multienzyme Complexes ,MESH: Archaea/genetics ,evolution ,MESH: Acetate-CoA Ligase/metabolism ,MESH: Multienzyme Complexes/metabolism ,MESH: Archaea/enzymology ,Bacteria ,MESH: Acetate-CoA Ligase/genetics ,Archaea ,acetogens ,030104 developmental biology ,chemistry ,biology.protein ,Genome, Bacterial - Abstract
Erratum in : Correction for Adam et al., Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. [Proc Natl Acad Sci U S A. 2018]; International audience; Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of un-cultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
- Published
- 2018
23. Methanogenesis and the Wood-Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association
- Author
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Simonetta Gribaldo, Panagiotis S. Adam, Guillaume Borrel, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Université Paris Diderot - Paris 7 (UPD7), G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. P.S.A. is supported by a PhD fellowship from Paris Diderot University and funds by the PhD Program 'Frontières du Vivant (FdV) – Programme Bettencourt., and Institut Pasteur [Paris] (IP)
- Subjects
0301 basic medicine ,MESH: Genome, Archaeal ,Methanogenesis ,Lineage (evolution) ,MESH: Archaea/metabolism ,[SDV]Life Sciences [q-bio] ,030106 microbiology ,Biology ,MESH: Wood/metabolism ,MESH: Methane/metabolism ,Evolution, Molecular ,MESH: Methanomicrobiaceae/genetics ,03 medical and health sciences ,Microbial ecology ,archaeal ancestor ,Genome, Archaeal ,Phylogenetics ,Phylogenomics ,MESH: Carbon/metabolism ,MESH: Evolution, Molecular ,Genetics ,MESH: Phylogeny ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,MESH: Methanomicrobiaceae/metabolism ,Ecology ,methanogenesis ,biology.organism_classification ,Wood ,Archaea ,Carbon ,MESH: Wood/chemistry ,030104 developmental biology ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,13. Climate action ,Evolutionary biology ,Wood–Ljungdahl pathway ,Wood-Ljungdahl pathway ,Methanomicrobiaceae ,Euryarchaeota ,Methane ,pathway loss ,MESH: Archaea/genetics ,Metabolic Networks and Pathways ,MESH: Metabolic Networks and Pathways/genetics ,Perspectives - Abstract
International audience; Methanogenesis coupled to the Wood-Ljungdahl pathway is one of the most ancient metabolisms for energy generation and carbon fixation in the Archaea. Recent results are sensibly changing our view on the diversity of methane-cycling capabilities in this Domain of Life. The availability of genomic sequences from uncharted branches of the archaeal tree has highlighted the existence of novel methanogenic lineages phylogenetically distant to previously known ones, such as the Methanomassiliicoccales. At the same time, phylogenomic analyses have suggested a methanogenic ancestor for all Archaea, implying multiple independent losses of this metabolism during archaeal diversification. This prediction has been strengthened by the report of genes involved in methane cycling in members of the Bathyarchaeota (a lineage belonging to the TACK clade), representing the first indication of the presence of methanogenesis outside of the Euryarchaeota. In light of these new data, we discuss how the association between methanogenesis and the Wood-Ljungdahl pathway appears to be much more flexible than previously thought, and might provide information on the processes that led to loss of this metabolism in many archaeal lineages. The combination of environmental microbiology, experimental characterization and phylogenomics opens up exciting avenues of research to unravel the diversity and evolutionary history of fundamental metabolic pathways.
- Published
- 2016
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