Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation

[1]  R. Amils Asgard, Archaea , 2021, Encyclopedia of Astrobiology.

[2]  M. Li,et al.  Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment , 2020, mSystems.

[3]  Filipa L. Sousa,et al.  Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota , 2019, mBio.

[4]  M. Li,et al.  Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes , 2019, mSystems.

[5]  Takashi Yamaguchi,et al.  Isolation of an archaeon at the prokaryote–eukaryote interface , 2019, Nature.

[6]  Fengping Wang,et al.  Metal-dependent anaerobic methane oxidation in marine sediment: Insights from marine settings and other systems , 2019, Science China Life Sciences.

[7]  B. Baker,et al.  New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea , 2019, Applied and Environmental Microbiology.

[8]  A. Spang,et al.  Asgard archaea capable of anaerobic hydrocarbon cycling , 2019, Nature Communications.

[9]  A. Spang,et al.  Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism , 2019, Nature Microbiology.

[10]  O. Béjà,et al.  Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche , 2019, Nature Microbiology.

[11]  M. Friedrich,et al.  CO2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments , 2019, bioRxiv.

[12]  M. Li,et al.  Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6 , 2019, Microbial Ecology.

[13]  M. Li,et al.  Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea) , 2018, The ISME Journal.

[14]  Donovan H. Parks,et al.  A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.) , 2018, The ISME Journal.

[15]  Volker Müller,et al.  Electron Bifurcation: A Long-Hidden Energy-Coupling Mechanism. , 2018, Annual review of microbiology.

[16]  Cindy J. Castelle,et al.  Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota , 2018, Nature Communications.

[17]  Itai Sharon,et al.  A distinct abundant group of microbial rhodopsins discovered using functional metagenomics , 2018, Nature.

[18]  Alexander J Probst,et al.  Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy , 2017, Nature Microbiology.

[19]  W. Inskeep,et al.  Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats , 2018, Nature Microbiology.

[20]  Lonnie D. Crosby,et al.  Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes , 2018, mSystems.

[21]  P. Forterre,et al.  Asgard archaea do not close the debate about the universal tree of life topology , 2018, PLoS genetics.

[22]  M. Li,et al.  Two or three domains: a new view of tree of life in the genomics era , 2018, Applied Microbiology and Biotechnology.

[23]  Eunsoo Kim,et al.  Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic , 2018, Nature Ecology & Evolution.

[24]  B. Baker,et al.  Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota , 2018, The ISME Journal.

[25]  H. Atomi,et al.  A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile , 2018, Science.

[26]  Tom O. Delmont,et al.  Linking pangenomes and metagenomes: the Prochlorococcus metapangenome , 2018, PeerJ.

[27]  M. Li,et al.  Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing , 2017, Front. Microbiol..

[28]  Thijs J. G. Ettema,et al.  Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life , 2017, Science.

[29]  P. Forterre,et al.  Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes , 2017, PLoS genetics.

[30]  Thijs J. G. Ettema,et al.  Asgard archaea illuminate the origin of eukaryotic cellular complexity , 2017, Nature.

[31]  S. Akanuma,et al.  Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids , 2016, Archaea.

[32]  Luis Pedro Coelho,et al.  Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper , 2016, bioRxiv.

[33]  Dianne K. Newman,et al.  The physiology of growth arrest: uniting molecular and environmental microbiology , 2016, Nature Reviews Microbiology.

[34]  Filipe M. Sousa,et al.  Exploring membrane respiratory chains. , 2016, Biochimica et biophysica acta.

[35]  Filipa L. Sousa,et al.  Lokiarchaeon is hydrogen dependent , 2016, Nature Microbiology.

[36]  M. Kanehisa,et al.  BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. , 2016, Journal of molecular biology.

[37]  B. Baker,et al.  Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction , 2016, The ISME Journal.

[38]  B. Baker,et al.  Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea , 2015, Nature Communications.

[39]  Neil D. Rawlings,et al.  Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors , 2015, Nucleic Acids Res..

[40]  C. Jackson,et al.  Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival , 2015, The ISME Journal.

[41]  Dongwan D. Kang,et al.  MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities , 2015, PeerJ.

[42]  E. Bergantino,et al.  [NiFe]-hydrogenase is essential for cyanobacterium Synechocystis sp. PCC 6803 aerobic growth in the dark , 2015, Scientific Reports.

[43]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[44]  J. W. Peters,et al.  [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation. , 2015, Biochimica et biophysica acta.

[45]  Thijs J. G. Ettema,et al.  Complex archaea that bridge the gap between prokaryotes and eukaryotes , 2015, Nature.

[46]  Yong Zhang,et al.  Shallow-ocean methane leakage and degassing to the atmosphere: triggered by offshore oil-gas and methane hydrate explorations , 2015, Front. Mar. Sci..

[47]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[48]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[49]  C. Schleper,et al.  Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge , 2013, Front. Microbiol..

[50]  Virginia P. Edgcomb,et al.  Gene expression in the deep biosphere , 2013, Nature.

[51]  S. Eddy,et al.  Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions , 2013, Nucleic acids research.

[52]  Hélène Touzet,et al.  SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data , 2012, Bioinform..

[53]  T. Miyatake,et al.  Depth-Related Differences in Organic Substrate Utilization by Major Microbial Groups in Intertidal Marine Sediment , 2012, Applied and Environmental Microbiology.

[54]  T. J. Smith,et al.  Organic carbon burial rates in mangrove sediments: Strengthening the global budget , 2012 .

[55]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[56]  A. Teske,et al.  Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages , 2012, Front. Microbio..

[57]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[58]  Elmar Pruesse,et al.  SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes , 2012, Bioinform..

[59]  Carlos M. Duarte,et al.  A blueprint for blue carbon: toward an improved understanding of the role of vegetated coastal habitats in sequestering CO2 , 2011 .

[60]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[61]  N. Marbà,et al.  Seagrass sediments as a global carbon sink: Isotopic constraints , 2010 .

[62]  Alexis Criscuolo,et al.  BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments , 2010, BMC Evolutionary Biology.

[63]  Martin Ester,et al.  PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes , 2010, Bioinform..

[64]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[65]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[66]  Konstantinos D. Tsirigos,et al.  Prediction of signal peptides in archaea. , 2008, Protein engineering, design & selection : PEDS.

[67]  Suzanne M. Paley,et al.  The MetaCyc database of metabolic pathways and enzymes , 2017, Nucleic Acids Res..

[68]  D. Burdige Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets? , 2007, Chemical reviews.

[69]  Rika Anderson,et al.  Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[70]  K. Nealson,et al.  Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk , 2003, Applied and Environmental Microbiology.

[71]  K. Horikoshi,et al.  Archaeology of Archaea: geomicrobiological record of Pleistocene thermal events concealed in a deep-sea subseafloor environment , 2001, Extremophiles.

[72]  C. Vetriani,et al.  Population Structure and Phylogenetic Characterization of Marine Benthic Archaea in Deep-Sea Sediments , 1999, Applied and Environmental Microbiology.

[73]  K. Horikoshi,et al.  Genetic diversity of archaea in deep-sea hydrothermal vent environments. , 1999, Genetics.

[74]  D. Kelleher,et al.  The essential OST2 gene encodes the 16-kD subunit of the yeast oligosaccharyltransferase, a highly conserved protein expressed in diverse eukaryotic organisms , 1995, The Journal of cell biology.

[75]  J. Kristjánsson,et al.  Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi Comb. nov.: Facultatively Aerobic, Extremely Acidophilic Thermophilic Sulfur-Metabolizing Archaebacteria , 1986 .

[76]  B. Jørgensen,et al.  A comparison of oxygen, nitrate, and sulfate respiration in coastal marine sediments , 1979, Microbial Ecology.

[77]  B. Mcguinness,et al.  Twenty years on. , 1976, British medical journal.

[78]  Seweryn Malgorzata,et al.  to Primordial , 2018 .

[79]  J. Damsté,et al.  Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’ , 2017, Environmental microbiology.

[80]  Y. Konishi,et al.  Kinetics of the Bioleaching of Chalcopyrite Concentrate by Acidophilic Thermophile Acidianus brierleyi , 1999, Biotechnology progress.