DEEM : Diversity, Ecology and Evolution of Microbes

Datasets · Software

Publications

2024

Gutiérrez-Preciado A, Dede, Baker BA, Eme L, Moreira D, Lopez-Garcia P (2024) Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines Nature Ecol Evol,8: pages 1856–1869
Prokina KI, Yubuki N, Tikhonenkov EV, Ciobanu MC, Lopez-Garcia P, Moreira D (2024) Refurbishing the marine parasitoid order Pirsoniales with newly (re)described marine and freshwater free-living predators J Euk Microbiol, 00: e13061 (early view)
Moreira D, Blas J, Kim E, Eme L (2024) A gene-rich mitochondrion with a unique ancestral protein transport system Curr Biol, 34: P3812-3819.e3
Baker BA, Gutierrez-Preciado A, Rodriguez del Rio A, McCarthy CGP, Lopez-Garcia P, Huerta-Cepas J, Susko E, Eme L, Moreira D (2024) Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments Nature Microbiol, 9: 964–975
Cubillos CF, Aguilar P, Moreira D, Bertolino P, Iniesto M, Dorador C, Lopez-Garcia P (2024) Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland Microbiology Spectrum, 12: e00072-24
Bacchetta T, López-García P, Gutiérrez-Preciado A, Mehta N, Skouri-Panet F, Benzerara K, Ciobanu, M, Yubuki N, Tavera R, Moreira D (2024) Description of Gloeomargarita ahousahtiae sp. nov. (Gloeomargaritales), a thermophilic cyanobacterium with intracellular carbonate inclusions Eur J Phycol, 59: 11-20
Cho A, Tikhonenkov DV, Lax G, Prokina KI, Keeling PJ (2024) Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean Mol Phyl Evol, 190: 107964
Prokina K, Tikhonenkov D, Lopez-Garcia P, Moreira D (2024) Morphological and molecular characterization of a new member of the phylum Rhodelphidia J Euk Microbiol, 71: e12995
Ramos JL, de Lorenzo V, López-García P (2024) Meeting Report: Microbes as Safeguards of the Environment Sustainable Microbiology, 1: qvae013
Timmis K, Hallsworth JE, McGenity TJ, Armstrong R, Colom MF, Karahan ZC, Chavarría M, Bernal P, Boyd ES, Ramos JL, Kaltenpoth M, Pruzzo C, Clarke G, López-Garcia P, Yakimov MM, Perlmutter J, Greening C, Eloe-Fadrosh E, Verstraete W, Nunes OC, Kotsyurbenko O, Nikel PI, Scavone P, Häggblom MM, Lavigne R, Le Roux F, Timmis JK, Parro V, Michán C, García JL, Casadevall A, Payne SM, Frey J, Koren O, Prosser JI, Lahti L, Lal R, Anand S, Sood U, Offre P, Bryce CC, Mswaka AY, Jores J, Kaçar B, Blank LM, Maaßen N, Pope PB, Banciu HL, Armitage J, Lee SY, Wang F, Makhalanyane TP, Gilbert JA, Wood TK, Vasiljevic B, Soberón M, Udaondo Z, Rojo F, Tamang JP, Giraud T, Ropars J, Ezeji T, Müller V, Danbara H, Averhoff B, Sessitsch A, Partida-Martínez LP, Huang W, Molin S, Junier P, Amils R, Wu XL, Ron E, Erten H, de Martinis ECP, Rapoport A, Öpik M, Pokatong WDR, Stairs C, Amoozegar MA, Serna JG. (2024) A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society Microb Biotechnol 17: e14456.
Williams TA, Davin AA, Szánthó LL, Stamatakis A, Wahl NA, Woodcroft BJ, Soo RM, Eme L, Sheridan PO, Gubry-Rangin C, Spang A, Hugenholtz P, Szöllősi GJ (2024) Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution ISME J. 18:wrae129
Reñé A, Timoneda N, Khodami S, López-García P, Martinez P, Hoppenrath M (2024) Morpho-molecular characterization of sand-dwelling dinoflagellate communities from the German Wadden Sea and insights on their spatiotemporal distribution Eur J Phycol, 59: 196-217
Banos H, Wong TKF, Daneau J, Susko E, Minh BQ, Lanfear R, Brown MW, Eme L, Roger AJ (2024) GTRpmix: A linked general-time reversible model for profile mixture models Mol Biol Evol, 19:msae174
Jones RE, Tice AK, Eliáš M, Eme L, Kolísko M, Nenarokov S, Pánek T, Rokas A, Salomaki E, Strassert JFH, Shen XX, Žihala D, Brown MW (2024) Create, analyze, and visualize phylogenomic datasets using PhyloFisher Curr Protoc. 4:e969
Eme L, Tamarit D (2024) Microbial diversity and open questions about the Deep Tree of Life Genome Biol Evol. 16:evae053
Boukheloua R, Mukherjee I, Park H, Šimek K, Kasalický V, Ngochera M, Grossart HP, Picazo-Mozo A, Camacho A, Cabello-Yeves PJ, Rodriguez-Valera F, Callieri C, Andrei AS, Pernthaler J, Posch T, Alfreider A, Sommaruga R, Hahn MW, Sonntag B, Lopez-Garcia P, Moreira D, Jardillier L, Lepère C, Biderre-Petit C, Bednarska A, Ślusarczyk M, Tóth VR, Banciu HL, Kormas K, Orlic S, Šantić D, Muyzer G, Herlemann DPR, Tammert H, Bertilsson S, Langenheder S, Zechmeister T, Salmaso N, Storelli N, Capelli C, Lepori F, Lanta V, Vieira HH, Kostanjšek F, Kabeláčová K, Chiriac MC, Haber M, Shabarova T, Fernandes C, Rychtecký P, Znachor P, Szőke-Nagy T, Layoun P, Wong HL, Kavagutti VS, Bulzu PA, Salcher MM, Piwosz K, Ghai R (2024) Global freshwater distribution of Telonemia protists ISME J. 20:wrae177. doi: 10.1093/ismejo/wrae177.
A. Foubert, D. Keir, B. Atnafu, T. Kidane and the ADD-ON Workshop Consortium (2024) Workshop report ADD-ON: Afar Dallol Drilling - ONset of sedimentary processes in an active rift basin Sci. Drilling. 33: 207–218.

2023

López-García P, Gutiérrez-Preciado A, Krupovic M, Ciobanu M, Deschamps P, Jardillier L, López-Pérez M, Rodríguez-Valera F, Moreira D (2023) Metagenome-derived virus-microbe ratios across ecosystems ISME J. 17: 1552-1563
López-García P, Moreira D (2023) The symbiotic origin of the eukaryotic cell C R Biol, 346: 55-73
Malaterre C, Javaux EJ, López-García P (2023) Misconceptions in Science Perspectives on Science, 31: 717-743.
Eme L, Tamarit D, Caceres EF, Stairs CW, De Anda V, Schön ME, Seitz KW, Dombrowski N, Lewis WH, Homa F, Saw JH, Lombard J, Nunoura T, Wen-Jun L, Hua ZS, Chen LX, Banfield JF, St John E, Reysenbach AL, Stott MB, Schramm A, Kjeldsen KU, Teske AP, Baker BJ, Ettema TJG (2023) Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes Nature, 618: 992-999
Yubuki N, Torruella G, Glindo LJ, Heiss AA, Ciobanu MC, Shiratoir T, Ishida K, Blas J, Kim E, Moreira D, Lopez-Garcia P, Eme L (2023) Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida J Euk Microbiol 70: e12997
Galindo LJ, Torruella G, López-García P, Ciobanu M, Gutiérrez-Preciado A, Karpov SA, Moreira D (2023) Phylogenomics supports the monophyly of aphelids and fungi and identifies new molecular synapomorphies Syst Biol, 3: 505–515.
Muller E, Rapin W, Caumartin J, Jézéquel D, De Wever A, Thomazo C, Havas R, López-García P, Moreira D, Tavera R, Benzerara K (2023) Diagenetic formation of stevensite by replacement of diatom frustules in the sediments of the alkaline Lake Alchichica (Mexico) Sedimentology, 70: 1013-1038
Galindo LJ, Prokina K, Torruella G, López-García P, Moreira D (2023) Maturases and group II introns in the mitochondrial genomes of the deepest jakobid branch Genome Biol Evol, 15: evad058.
Caumartin J, Benzerara K, Havas R, Thomazo C, López-García P, Duprat E (2023) The chemical conditions necessary for the formation of microbialites Geochem Persp Let, 25: 30–35
Babajanyan SG, Wolf YI, Khachatryan A, Allahverdyan A, López-García P, Koonin EV (2023) Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes Proc Natl Acad Sci U S A, 120: e2301522120
Torruella G, Galindo LA, Moreira D, Ciobanu M, Heiss AA, Yubuki N, Kim E, López-García P (2023) Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists J Euk Microbiol, 70: e12956
Christaki U, Skouroliakou D-I, Jardillier L (2023) Interannual dynamics of putative parasites (Group II Syndiniales) in a coastal ecosystem Environ Microbiol, 25: 1314-1328
Gaëtan J, Halary S, Millet M, Bernard C, Duval C, Hamlaoui S, Hecquet A, Gugger M, Marie B, Mehta N, Moreira D, Skouri-Panet F, Travert C, Duprat E, Leloup J, Benzerara K. (2023) Widespread formation of intracellular calcium carbonates by the bloom-forming cyanobacterium Microcystis. Environ Microbiol. 25: 751-765.
Havas R, Thomazo C, Iniesto M, Jézéquel D, Moreira D, Tavera R, Caumartin J, Muller E, López-García P, Benzerara K (2023) Biogeochemical processes captured by carbon isotopes in redox-stratified water columns: a comparative study of four modern stratified lakes along an alkalinity gradient Biogeosci. 20: 2347-2367.
Havas R, Thomazo C, Iniesto M, Jézéquel D, Moreira D, Tavera R, Caumartin J, Muller E, López-García P, Benzerara K (2023) The hidden role of dissolved organic carbon in the biogeochemical cycle of carbon in modern redox-stratified lakes Biogeosci. 20: 2405–2424.
Blaz J, Galindo LJ, Heiss AA, Kaur H, Torruella G, Yang A, Alexa Thompson L, Filbert A, Warring S, Narechania A, Shiratori T, Ishida KI, Dacks JB, López-García P, Moreira D, Kim E, Eme L (2023) One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade. Sci Data, 10: 603
Benzerara K, Agnes E, Ciobanu , De Wever A, Bertolino P, Iniesto M, Jezequel D, López-García P, Menguy N, Muller E, Skouri-Panet F, Swaraj S, Tavera R, Thomazo C, Moreira D (2023) Biomineralization of amorphous Fe-, Mn- and Si-rich mineral phases by cyanobacteria under oxic and alkaline conditions Biogeosci. 20: 4183–4195.
Novák LVF, Treitli SC, Pyrih J, Hałakuc P, Pipaliya SV, Vacek V, Brzoň O, Soukal P, Eme L, Dacks JB, Karnkowska A, Eliáš M, Hampl V (2023) Genomics of Preaxostyla flagellates illuminates the path towards the loss of mitochondria. PLoS Genet. 19: e1011050
Courseaux A, George O, Deschamps P, Bompard C, Duchêne T, Dauvillée D (2023) BE3 is the major branching enzyme isoform required for amylopectin synthesis in Chlamydomonas reinhardtii Front Plant Sci. 14:1201386

2022

Iniesto M, Moreira D, Benzerara K, Reboul G, Bertolino P, Tavera R, Lopez-Garcia P (2022) Planktonic microbial communities from microbialite-bearing lakes sampled along a salinity-alkalinity gradient Limnol Oceanogr, 67: 2718-2733
Galindo LJ, López-García P, Moreira D (2022) First molecular characterization of the elusive marine protist Meteora sporadica Protist, 173: 125896
Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A (2022) A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution Nature Ecol Evol, 6: 1007–1023
Muñoz-Gómez SA, Susko E, Williamson K, Eme L, Slamovits CH, Moreira D, López-García P, Roger AJ (2022) Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria Nature Ecol Evol, 6: 253–262
Benzerara K, Duprat E, Bitard-Feildel T, Caumes G, Cassier-Chauvat C, Chauvat F, Dezi M, Diop SI, Gaschignard G, Gorgen S, Gugger M, Lopez-Garcıa P, Millet M, Skouri-Panet F, Moreira D, Callebaut I (2022) A new gene family diagnostic for intracellular biomineralization of amorphous Ca carbonates by Cyanobacteria Genome Biol Evol, 14: evac026
Belilla J, Iniesto M, Moreira D, Benzerara K, Gérard E, López-García JM, Kotopoulou E, López-García P (2022) Active microbial airborne dispersal and biomorphs as confounding factors for life detection in the cell-degrading brines of the polyextreme Dallol geothermal field. mBio 13: e00307-22
van Beveren F, Eme L, López-García P, Ciobanu M, Moreira D (2022) Independent size expansions and intron proliferation in red algal plastid and mitochondrial genomes Genome Biol Evol. 14:evac037
Zhang X, Hu Y, Eme L, Maruyama S, Eveleigh RJM, Curtis BA, Sibbald SJ, Hopkins JF, Filloramo GV, van Wijk KJ, Archibald JM (2022) TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets STAR Protoc. 3:101175
Tamarit D, Caceres EF, Krupovic M, Nijland R, Eme L, Robinson NP, Ettema TJG (2022) A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses Nature Micro, 7: 948–952
Tikhonenkov DV, Jamy M, Borodina AS, Belyaev AO, Zagumyonnyi DG, Prokina KI, Mylnikov AP, Burki F, Karpov SA. (2022) On the origin of TSAR: morphology, diversity and phylogeny of Telonemia. Open Biol. 12: 210325
Schavemaker PE, Muñoz-Gómez SA. (2022) The role of mitochondrial energetics in the origin and diversification of eukaryotes. Nature Ecol Evol. 6: 1307-1317
Tikhonenkov DV, Mikhailov KV, Gawryluk RMR, Belyaev AO, Mathur V, Karpov SA, Zagumyonnyi DG, Borodina AS, Prokina KI, Mylnikov AP, Aleoshin VV, Keeling PJ (2022) Microbial predators form a new supergroup of eukaryotes Nature. 612: 714-719
Eme L, Stairs CW (2022) Life through the lens of metabolism Nature Ecol Evol. 6: 1590

2021

Muñoz-Gómez SA, Kreutzand M, Hess S (2021) A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts Science Advances, 7: eabg4102
Galindo LJ, López-García P, Torruella G, Karpov S, Moreira D (2021) Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota Nature Communications, 12: 4973.
Belilla J, Iniesto M, Moreira D, Benzerara K, López-García JM, López-Archilla AI, Reboul G, Deschamps P, Gérard E, López-García P (2021) Archaeal overdominance close to life-limiting conditions in geothermally influenced hypersaline lakes at the Danakil Depression, Ethiopia Environ Microbiol, 23: 7168-7182
Moreira D, Zivanovic Y, López-Archilla AI, Iniesto M, López-García P. (2021) Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii Nature Communications, 12: 2454
Iniesto M, Moreira D, Benzerara K, Muller E, Bertolino P, Tavera R, López-García P (2021) Rapid formation of mature microbialites in Lake Alchichica, Mexico Environ Microbiol Rep, 13:600-605
Reboul G, Moreira D, Annenkova N, Bertolino P, Vershinin KE, López-García P (2021) Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake ISME J, 15:3412–3417
David GM, Moreira D, Reboul G, Annenkova NV, Galindo LJ, Bertolino P, López-Archilla AI, Jardillier L, López-García P. (2021) Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake. Environ Microbiol, 23: 1436-1451
Koreny L , Zeeshan M , Barylyuk K, Tromer EC , van Hooff JJE , Brady D , Ke H, Chelaghma S, Ferguson DJP, Eme L, Tewari R, Waller RF (2021) Molecular characterization of the conoid complex in Toxoplasma reveals its conservation in all apicomplexans, including Plasmodium species PLoS Biol, 19:e3001081
Iniesto M, Gutierrez-Silva P, Dias JJ, Carvalho S, Buscalioni AD, Lopez-Archilla AI (2021) Soft tissue histology of insect larvae decayed in laboratory experiments using microbial mats: Taphonomic comparison with Cretaceous fossil insects from the exceptionally preserved biota of Araripe, Brazil. Palaeogeography, Palaeoclimatology, Palaeoecology. 564: 110156
López-García P, Moreira D (2021) Physical connections: prokaryotes parasitizing their kin Environ Microbiol Rep 13, 54–61
Iniesto M, Moreira D, Reboul G, Deschamps P, Benzerara K, Bertolino P, Saghaï A, Tavera R, López-García P (2021) Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient Environ Microbiol, 23: 51-68
Christaki U, Guenegues A, Liu Y, Blain S, Catala P, Debeljak P, Jardillier L, Irion S, Planchon F, Sassenhagen I, Sime-Ngando T, Obernosterer I (2021) Seasonal microbial food web dynamics in contrasting Southern Ocean productivity regimes Limnol Oceanogr 66: 108-122
Irion S, Christaki U, Berthelot H, L’Helguen S, Jardillier L (2021) Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean ISME J 15: 2509–2522
David G, López-García P, Moreira D, Alric B, Deschamps P, Bertolino P, Restoux G, Rochelle-Newall E, Thébault E, Simon M, Jardillier L (2021) Similar temporal patterns despite dissimilar prokaryotic and protist communities in small freshwater systems Mol Ecol, 30:2162–2177
Reñé A, Hoppenrath M, Reboul G, Moreira D, López-García P (2021) Composition and temporal dynamics of sand-dwelling dinoflagellate communities from three Mediterranean beaches Aquat Microb Ecol, 86: 85–98
Christaki U, Skouroliakou I-D, Delegrange A, Irion S, Courcot L, Jardillier L, Sassenhagen I (2021) Microzooplankton diversity and potential role in carbon cycling of contrasting Southern Ocean productivity regimes Journal of Marine Systems, 219: 103531
Zeyen N, Benzerara K, Beyssac O, Daval D, Muller E, Thomazo C, Tavera R, Lopez-Garcia P, Moreira D, Duprat E (2021) Integrative analysis of the mineralogical and chemical composition of modern microbialites from ten Mexican lakes: What do we learn about their formation? Geochim Cosmochim Acta, 305:148–184
Lax G, Kolisko M, Eglit Y, Lee WJ, Yubuki N, Karnkowska A, Leander BS, Burger G, Keeling PJ, Simpson AGB (2021) Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs Mol Phylogenet Evol, 159:107088
Žárský V, Klimeš V, Pačes J, Vlček Č, Hradilová M, Beneš V, Nývltová E, Hrdý I, Pyrih J, Mach J, Barlow L, Stairs CW, Eme L, Hall N, Eliáš M, Dacks JB, Roger A, Tachezy J (2021) The Mastigamoeba balamuthi genome and the nature of the free-living ancestor of Entamoeba Mol Biol Evol. 38:2240-2259
Tice AK, Žihala D, Pánek T, Jones RE, Salomaki ED, Nenarokov S, Burki F, Eliáš M, Eme L, Roger AJ, Rokas A, Shen XX, Strassert JFH, Kolísko M, Brown MW (2021) PhyloFisher: A phylogenomic package for resolving eukaryotic relationships PLoS Biol. 19:e3001365
Stairs CW, Táborský P, Salomaki ED, Kolisko M, Pánek T, Eme L, Hradilová M, Vlček Č, Jerlström-Hultqvist J, Roger AJ, Čepička I (2021) Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes Curr Biol. S0960-9822(21)01364-6
Olvera-Vazquez SG, Remoué C, Venon A, Rousselet A, Grandcolas O, Azrine M, Momont L, Galan M, Benoit L, David GM, Alhmedi A, Beliën T, Alins G, Franck P, Haddioui A, Jacobsen SK, Andreev R, Simon S, Sigsgaard L, Guibert E, Tournant L, Gazel F, Mody K, Khachtib Y, Roman A, Ursu TM, Zakharov IA, Belcram H, Harry M, Roth M, Simon JC, Oram S, Ricard JM, Agnello A, Beers EH Engelman J, Balti I, Salhi-Hannachi A, Zhang H, Tu H, Mottet C, Barrès B, Degrave A, Razmjou J, Giraud T, Falque M, Dapena E, Miñarro M, Jardillier L, Deschamps P, Jousselin E, Cornille A (2021) Large-scale geography survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa Peer Community Journal, 1, article no. e34

2020

Saghaï A, Zivanovic Y, Moreira D, Tavera R, López-García P (2020) A novel microbialite-associated phototrophic Chloroflexi lineage exhibiting a quasi-clonal pattern along depth Genome Biol Evol. 12:1207-1216
López-García P, Moreira D (2020) The Syntrophy hypothesis for the origin of eukaryotes revisited Nature Microbiol, 5: 655–667
López-García P, Moreira D (2020) Cultured Asgard archaea shed light on eukaryogenesis Cell, 181: 232-235
Lopez-Garcia JM, Moreira D, Benzerara K, Grunewald O, López-García P (2020) Origin and evolution of the halo-volcanic complex of Dallol: Proto-volcanism in Northern Afar (Ethiopia) Front Earth Sci 7: 351
Yubuki N, López-García P, Reboul G, Brown MW, Pollet N, Moreira D (2020) Ancient adaptive lateral gene transfers in the symbiotic Opalina - Blastocystis stramenopile lineage Mol Biol Evol, 37:651-659
Sassenhagen I, Irion S, Jardillier L, Moreira D, Christaki U (2020) Protist interactions and community structure during early autumn in the Kerguelen region (Southern Ocean) Protist, 171:125709
Reñé A, Auladell A, Reboul G, Moreira D, López-García P (2020) Performance of the melting seawater‐ice elution method on the metabarcoding characterization of benthic protist communities Environ Microbiol Rep, 12:314-323
Massoni J, Bortfeld-Miller M, Jardillier L, Salazar G, Sunagawa S, Vorholt JA (2020) Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species ISME J. 14:245-258
Dharamshi JE, Tamarit D, Eme L, Stairs CW, Martijn J, Homa F, Jørgensen SL, Spang A, Ettema TJG (2020) Marine sediments illuminate Chlamydiae diversity and evolution Curr Biol. 30:1032-1048
Reñé A, Satta CT, López-García P, Hoppenrath M (2020) Re-evaluation of Amphidiniopsis (Dinophyceae) morphogroups based on phylogenetic relationships and description of three new sand-dwelling species from the NW Mediterranean J Phycol, 56:68-84
Schön ME, Eme L, Ettema TJG (2020) PhyloMagnet: Fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics Bioinformatics, 36:1718–1724
Sibbald SJ, Eme L, Archibald JM, Roger AJ (2020) Lateral gene transfer mechanisms and pan-genomes in eukaryotes Trends Parasitol. 36:927-941
Salomaki ED, Eme L, Brown MW, Kolisko M (2020) Releasing uncurated datasets is essential for reproducible phylogenomics. Nat Ecol Evol. doi:10.1038/s41559-020-01296-w
Stairs CW, Sharamshi JE, Tamarit D, Eme L, Jørgensen SL, Spang A, Ettema TJG (2020) Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. Sci Adv. 6:eabb7258.
Vosseberg J, van Hooff JJE, Marcet-Houben M, van Vlimmeren A, van Wijk LM, Gabaldón T, Snel B. (2020) Timing the origin of eukaryotic cellular complexity with ancient duplications. Nat Ecol Evol. doi:10.1038/s41559-020-01320-z.
Karpov SA, Vishnyakov AE, López-García P, Zorina NA, Ciobanu M, Tcvetkova VS, Moreira D (2020) Morphology and molecular phylogeny of Aphelidium insulamus sp. nov. (Aphelida, Opisthosporidia) Protistology. 14:191–203
Irion S, Jardillier L, Sassenhagen I, Christaki U (2020) Marked spatio-temporal variations in small phytoplankton structure in contrasted waters of the Southern Ocean (Kerguelen area) Limnol Oceanogr doi: 10.1002/lno.11555
Bouchard F, Agnan F, Bröder L, Fouché L, Hirst C, Sjöberg Y & the SPLASH team (2020) The SPLASH Action Group – Towards standardized sampling strategies in permafrost science Adv Polar Sci, 31: 153-155

2019

Muñoz-Gómez SA, Durnin K, Eme L, Paight C, Lane CE, Saffo MB, Slamovits CH (2019) Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts Genome Biol Evol. 11:2727-2740
Belilla J, Moreira D, Jardillier J, Reboul G, Benzerara K, Lopez-Garcia JM, Bertolino P, Lopez-Archilla AI, López-García P (2019) Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area. Nature Ecol Evol, 3:1552–1561
Ponce-Toledo RI, López-García P, Moreira D. (2019) Horizontal and endosymbiotic gene transfer in early plastid evolution New Phytol, 224: 618-624
López-García P, Moreira D. (2019) Eukaryogenesis, a syntrophy affair Nat Microbiol. 4:1068-1070.
Moreira D, López-García P. (2019) Time series are critical to understand microbial plankton diversity and ecology Mol Ecol, 28:920-922
Monteil CL, Vallenet D, Menguy N, Benzerara K, Barbe V, Fouteau S, Cruaud C, Floriani M, Viollier E, Adryanczyk G, Leonhardt N, Faivre D, Pignol D, López-García P, Weld RJ, Lefevre CT (2019) A symbiotic origin of magnetoreception in unicellular eukaryotes Nat Microbiol. 4:1088-1095
Lepère C, Domaizon I, Humbert JF, Jardillier L, Hugoni M, Debroas D. (2019) Diversity, spatial distribution and activity of fungi in freshwater ecosystems PeerJ. 7:e6247.
Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, Del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q. (2019) Revisions to the classification, nomenclature, and diversity of eukaryotes J Eukaryot Microbiol. 66:4-119.
Reboul G, Moreira D, Bertolino P, Hillebrand-Voiculescu A, López-García P (2019) Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania Environ Microbiol Rep, 11:464-473
Zeyen N, Benzerara K, Menguy N, Brest J, Templeton A, Webb S, Gérard E, Moreira D, López-García P, Tavera R, Morin G. (2019) Fe-bearing phases in modern lacustrine microbialites from Mexico Geochim. Cosmochim. Acta. 253:201-230.
Karpov SA, Moreira D, Mamkaeva MA, Popova OV, Aleoshin VV, López-García P (2019) New member of Gromochytriales (Chytridiomycetes) – Apiochytrium granulosporum nov. gen. et sp. 66: 582–591
Karpov SA, Vishnyakov AE, Moreira D, López-García P. (2019) The ultrastructure of Sanchytrium tribonematis (Sanchytriaceae, Fungi incertae sedis) confirms its close relationship to Amoeboradix. J Eukaryot Microbiol. 66:892-898
Galindo LJ, Torruella G, Moreira D, Eglit Y, Simpson AGB, Völcker E, Clauss S, López-García P (2019) Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of Fungi Philos Trans R Soc Lond B Biol Sci. 374:20190094
Iniesto M, Thomazo C, Fara E, Team PB (2019) Deciphering the exceptional preservation of the Early Triassic Paris Biota (Bear Lake County, Idaho, USA) Geobios, 54, 81-93.

2018

Torruella G, Grau-Bové X, Moreira D, Karpov SA, Burns J, Sebé-Pedrós A, Völker E, López-García P (2018) Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi Communications Biology, 1:231
Gutiérrez-Preciado A*, Saghaï A*, Moreira D, Zivanovic Y, Deschamps P, López-García P (2018) Functional shifts in microbial mats recapitulate early Earth metabolic transitions Nature Ecol Evol, 2:1700-1708
Cam N, Benzerara K, Georgelin T, Jaber M, Lambert JF, Poinsot M, Skouri-Panet F, Moreira D, López-García P, Raimbault E, Cordier L, Jézéquel D (2018) Cyanobacterial formation of intracellular Ca-carbonates in undersaturated solutions Geobiology, 16: 49-61
Galindo LJ, Torruella G, Moreira D, Timpano H, Paskerova G, Smirnov A, Nassonova E, López-García P. (2018) Evolutionary genomics of Metchnikovella incurvata (Metchnikovellidae): An early branching microsporidium Genome Biol Evol. 10:2736-2748.
Ponce-Toledo RI, Moreira D, López-García P, Deschamps P. (2018) Secondary plastids of euglenids and chlorarachniophytes function with a mix of genes of red and green algal ancestry Mol. Biol. Evol. 35: 2198–2204.
Karpov SA, López-García P, Mamkaeva MA, Klimov VI, Vishnyakov AE, Tcvetkova VS, Moreira D. (2018) The chytrid-like parasites of algae Amoeboradix gromovi gen. et sp. nov. and Sanchytrium tribonematis belong to a new fungal lineage Protist. 169:122-140.
López-Escardó D, López-García P, Moreira D, Ruiz-Trillo I, Torruella G. (2018) Parvularia atlantis gen. et sp. nov., a nucleariid filose amoeba (Holomycota, Opisthokonta) J Eukaryot Microbiol. 65:170-179.
Longo WM, Huang YS, Yao Y, Zhao JJ, Giblin AE, Wang X, Zech R, Haberzettl T, Jardillier L, Toney J, Liu ZH, Krivonogov S, Kolpakova M, Chu GQ, D'Andrea WJ, Harada N, Nagashima K, Sato M, Yonenobu H, Yamada K, Gotanda K, Shinozuka Y. (2018) Widespread occurrence of distinct alkenones from Group I haptophytes in freshwater lakes: Implications for paleotemperature and paleoenvironmental reconstructions Earth Planet. Sci. Lett. 492:239-250 .
Rochelle-Newall E, Niboyet A, Jardillier L, Fiorini S, Chollet S, Llavata M, de Santis E, Barot S, Lacroix G. (2018) Impacts of elevated atmospheric CO2 concentration on terrestrial-aquatic carbon transfer and a downstream aquatic microbial community Aquat. Sci. 80:UNSP30.
Bass D, Czech L, Williams BAP, Berney C, Dunthorn M, Mahé F, Torruella G, Stentiford GD, Williams TA. (2018) Clarifying the relationships between Microsporidia and Cryptomycota J Eukaryot Microbiol. 65:773-782.
Mehrshad M, Rodriguez-Valera F, Amoozegar MA, López-García P, Ghai R. (2018) The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling ISME J. 12:655-668.
Rebollar EA, Gutiérrez-Preciado A, Noecker C, Eng A, Hughey MC, Medina D, Walke JB, Borenstein E, Jensen RV, Belden LK, Harris RN. (2018) The skin microbiome of the neotropical frog Craugastor fitzingeri: Inferring potential bacterial-host-pathogen interactions from metagenomic data. Front Microbiol. 9:466.
Iniesto M, Blanco-Moreno C, Villalba A, Buscalioni AD, Guerrero MC, López-Archilla AI (2018) Plant tissue decay in long-term experiments with microbial mats Geosciences, 8: 387.

2017

Haro-Moreno J, Rodriguez-Valera F, López-García P, Moreira D, Martin-Cuadrado AB (2017) Marine Group II New Insights into Marine Group III Euryarchaeota, from dark to light ISME J, 11:1102-1117
Moreira D, López-García P. (2017) Evolution: King-size plastid genomes in a new red algal clade Curr Biol. 27:R651-R653.
Saghaï A, Gutiérrez-Preciado A, Deschamps P, Moreira D, Bertolino P, Ragon M, López-García P. (2017) Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond Environ Microbiol. 19:2405-2421.
Moreira D, López-García P. (2017) Protist evolution: Stealing genes to gut it out Curr Biol. 27:R223-R225.
López-García P, Eme L, Moreira D. (2017) Symbiosis in eukaryotic evolution J Theor Biol. 434:20-33.
Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D. (2017) An early-branching freshwater cyanobacterium at the origin of plastids Curr Biol. 27:386-391.
Karpov SA, Torruella G, Moreira D, Mamkaeva MA, López-García P. (2017) Molecular phylogeny of Paraphelidium letcheri sp. nov. (Aphelida, Opisthosporidia) J Eukaryot Microbiol. 64:573-578.
Moreira D, Tavera R, Benzerara K, Skouri-Panet F, Couradeau E, Gérard E, Fonta CL, Novelo E, Zivanovic Y, López-García P. (2017) Description of Gloeomargarita lithophora gen. nov., sp. nov., a thylakoid-bearing, basal-branching cyanobacterium with intracellular carbonates, and proposal for Gloeomargaritales ord. nov. Int J Syst Evol Microbiol. 67:653-658
Torruella G, Moreira D, López-García P. (2017) Phylogenetic and ecological diversity of apusomonads, a lineage of deep-branching eukaryotes Environ Microbiol Rep. 9:113-119.
Karpov SA, Tcvetkova VS, Mamkaeva MA, Torruella G, Timpano H, Moreira D, Mamanazarova KS, López-García P. (2017) Morphological and genetic diversity of Opisthosporidia: New aphelid Paraphelidium tribonemae gen. et sp. nov. J Eukaryot Microbiol. 64:204-212.
Debroas D, Domaizon I, Humbert JF, Jardillier L, Lepère C, Oudart A, Taïb N. (2017) Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data FEMS Microbiol Ecol. 93:4.
Findinier J, Tunçay H, Schulz-Raffelt M, Deschamps P, Spriet C, Lacroix JM, Duchêne T, Szydlowski N, Li-Beisson Y, Peltier G, D'Hulst C, Wattebled F, Dauvillée D. (2017) The Chlamydomonas mex1 mutant shows impaired starch mobilization without maltose accumulation J Exp Bot. 68:5177-5189.
Grau-Bové X, Torruella G, Donachie S, Suga H, Leonard G, Richards TA, Ruiz-Trillo I. (2017) Dynamics of genomic innovation in the unicellular ancestry of animals Elife. 6:e26036.
Pachiadaki MG, Sintes E, Bergauer K, Brown J, Record N, Swan B, Hallam S, López-García P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R. (2017) Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation Science. 358:1046-1051.

2016

Derelle R, López-García P, Timpano H, Moreira D. (2016) A phylogenomic framework to study the diversity and evolution of Stramenopiles (=Heterokonts) Mol Biol Evol. 33:2890-2898.
Saghaï A, Zivanovic Y, Moreira D, Benzerara K, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. (2016) Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient Environ Microbiol. 18:4990-5004.
Simon M, López-García P, Deschamps P, Restoux G, Bertolino P, Moreira D, Jardillier L. (2016) Resilience of freshwater communities of small microbial eukaryotes undergoing severe drought events Front Microbiol. 7:812.
Gómez F, Takayama H, Moreira D, López-García P. (2016) Unarmoured dinoflagellates with a small hyposome: Torodinium and Lebouridinium gen. nov. for Katodinium glaucum (Gymnodiniales, Dinophyceae) Eur J Phycol. 51:226-241.
Iniesto M, Buscalioni ÁD, Carmen Guerrero M, Benzerara K, Moreira D, López-Archilla AI. (2016) Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates Sci Rep. 6:25716.
Li J, Margaret-Oliver I, Cam N, Boudier T, Blondeau M, Leroy E, Cosmidis J, Skouri-Panet F, Guigner JM, Ferard C, Poinsot M, Moreira D, López-García P, Cassier-Chauvat C, Chauvat F, Benzerara K. (2016) Biomineralization patterns of intracellular carbonatogenesis in cyanobacteria: Molecular hypotheses Minerals. 10:6.
Zeyen N, Daval D, López-García P, Moreira D, Gaillardet J, Benzerara K. (2016) Geochemical conditions allowing the formation of modern lacustrine microbialites Procedia Earth Planet. Sci. 17:380-383.
Karpov SA, López-García P, Mamkaeva MA, Vishnyakov AE, Moreira D. (2016) Chytridiomycete Polyphagus parasiticus: Molecular phylogeny supports the erection of a new chytridiomycete order Mycol. Phytopatol. 50:362-366.
Karpov SA, Mamkaeva MA, Moreira D, López-García P. (2016) Molecular phylogeny of Aphelidium tribonemae reveals its sister relationship with A. aff. melosirae (Aphelida, Opisthosporidia) Protistology. 10:97–103
Pašić L, Martin-Cuadrado AB, López-García P. (2016) "Deciphering archaeal communities" Omics tools in the study of archaeal communities Methods Mol Biol. 1399:1-28.
Lukeš J, López-García P, Louis E, Boekhout T. (2016) Meeting Report: Minutes from EMBO: Ten years of comparative genomics of eukaryotic microorganisms Protist.167:217-221.
del Campo J, Guillou L, Hehenberger E, Logares R, López-García P, Massana R. (2016) Ecological and evolutionary significance of novel protist lineages Eur J Protistol. 55:4-11.
Mizuno C, Ghai R, Saghaï A, López-García P, Rodriguez-Valera F. (2016) Genomes of abundant and widespread active viruses from the deep ocean mBio 7: e00805-16.

2015

Gómez F, López-García P, Takayama H, Moreira D. (2015) Balechina and the new genus Cucumeridinium gen. nov. (Dinophyceae), unarmored dinoflagellates with thick cell coverings J Phycol. 51:1088-105.
López-García P, Moreira D. (2015) Open questions on the origin of eukaryotes Trends Ecol Evol. 30:697-708.
Moreira D, López-García P. (2015) Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes? Philos Trans R Soc Lond B Biol Sci. 370:20140327.
Saghaï A, Zivanovic Y, Zeyen N, Moreira D, Benzerara K, Deschamps P, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. (2015) Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites Front Microbiol. 6:797.
López-García P, Zivanovic Y, Deschamps P, Moreira D. (2015) Bacterial gene import and mesophilic adaptation in archaea Nat Rev Microbiol. 13:447-456.
Simon M, López-García P, Deschamps P, Moreira D, Restoux G, Bertolino P, Jardillier L. (2015) Marked seasonality and high spatial variability of protist communities in shallow freshwater systems ISME J. 9:1941-1953.
Petitjean C, Deschamps P, López-García P, Moreira D, Brochier-Armanet C. (2015) Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life Mol Biol Evol. 32:1242-1254.
Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. (2015) A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum ISME J. 9:1619-1634.
Simon M, Jardillier L, Deschamps P, Moreira D, Restoux G, Bertolino P, López-García P. (2015) Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems Environ Microbiol. 17:3610-3627.
Roguet A, Laigle GS, Therial C, Bressy A, Soulignac F, Catherine A, Lacroix G, Jardillier L, Bonhomme C, Lerch TZ, Lucas FS. (2015) Neutral community model explains the bacterial community assembly in freshwater lakes FEMS Microbiol Ecol. 91:11.
Grob C, Jardillier L, Hartmann M, Ostrowski M, Zubkov MV, Scanlan DJ. (2015) Cell-specific CO2 fixation rates of two distinct groups of plastidic protists in the Atlantic Ocean remain unchanged after nutrient addition Environ Microbiol Rep. 7:211-218.
Szafranski KM, Deschamps P, Cunha MR, Gaudron SM, Duperron S. (2015) Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria Front Microbiol. 6:162.
Zeyen N, Benzerara K, Li J, Groleau A, Balan E, Robert J-L, Esteve I, Tavera R, Moreira D, López-García P. (2015) Formation of low-T hydrated silicates in modern microbialites from Mexico and implications for microbial fossilization Frontiers Earth Sci. 3:64.
Faure D, Bonin P, Duran R and the EC2CO consortium. (2015) Environmental microbiology as a mosaic of explored ecosystems and issues Environ Sci Pollut Res. 22:13577–13598.

2014

Petitjean C, Deschamps P, López-García P, Moreira D. (2014) Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota Genome Biol Evol. 7:191-204.
Ragon M, Benzerara K, Moreira D, Tavera R, López-García P. (2014) 16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization Front Microbiol. 5:331.
Benzerara K, Skouri-Panet F, Li J, Férard C, Gugger M, Laurent T, Couradeau E, Ragon M, Cosmidis J, Menguy N, Margaret-Oliver I, Tavera R, López-García P, Moreira D. (2014) Intracellular Ca-carbonate biomineralization is widespread in cyanobacteria Proc Natl Acad Sci U S A. 111:10933-10938.
Karpov SA, Mamkaeva MA, Benzerara K, Moreira D, López-García P. (2014) Molecular phylogeny and ultrastructure of Aphelidium aff. melosirae (Aphelida, Opisthosporidia) Protist. 165:512-526.
Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P. (2014) Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota Genome Biol Evol. 6:1549-1563.
Moreira D, López-García P. (2014) The rise and fall of Picobiliphytes: how assumed autotrophs turned out to be heterotrophs Bioessays. 36:468-474.
Bachy C, Moreira D, Dolan JR, López-García P. (2014) Seasonal dynamics of free-living tintinnid ciliate communities revealed by environmental sequences from the North-West Mediterranean Sea FEMS Microbiol Ecol. 87:330-342.
Moreira D, Deschamps P. (2014) What was the real contribution of endosymbionts to the eukaryotic nucleus? Insights from photosynthetic eukaryotes Cold Spring Harb Perspect Biol. 6:a016014.
Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AG, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ. (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing PLoS Biol. 12:e1001889
Deschamps P. (2014) Primary endosymbiosis: have cyanobacteria and Chlamydiae ever been roommates? Acta Soc. Bot. Pol. 83:291-302 .
Barbieri R, Cavalazzi B, Stivaletta N, López-García P. (2014) Silicified biota in high-altitude geothermally-influenced ignimbrites at El Tatio Geyser Field (Andean Cordillera, Chile) Geomicrobiol J. 31:493–508.
Amarouche-Yala S, Benouadah A, El Ouahab Bentabet A, López-García P. (2014) Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs Extremophiles. 18:1035-1047.

2013

Gérard E, Ménez B, Couradeau E, Moreira D, Benzerara K, Tavera R, López-García P. (2013) Specific carbonate-microbe interactions in the modern microbialites of Lake Alchichica (Mexico) ISME J. 7:1997-2009.
Simon M, López-García P, Moreira D, Jardillier L. (2013) New haptophyte lineages and multiple independent colonizations of freshwater ecosystems Environ Microbiol Rep. 5:322-332.
Ragon M, Van Driessche AE, García-Ruíz JM, Moreira D, López-García P. (2013) Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico Front Microbiol. 4:37.
Bachy C, Dolan JR, López-García P, Deschamps P, Moreira D. (2013) Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study ISME J. 7:244-255.
Kirkham AR, Lepère C, Jardillier LE, Not F, Bouman H, Mead A, Scanlan DJ. (2013) A global perspective on marine photosynthetic picoeukaryote community structure ISME J. 7:922-936.
Collén J, Porcel B, Carré W, Ball SG, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B, Valentin K, Elias M, Artiguenave F, Arun A, Aury JM, Barbosa-Neto JF, Bothwell JH, Bouget FY, Brillet L, Cabello-Hurtado F, Capella-Gutiérrez S, Charrier B, Cladière L, Cock JM, Coelho SM, Colleoni C, Czjzek M, Da Silva C, Delage L, Denoeud F, Deschamps P, Dittami SM, Gabaldón T, Gachon CM, Groisillier A, Hervé C, Jabbari K, Katinka M, Kloareg B, Kowalczyk N, Labadie K, Leblanc C, Lopez PJ, McLachlan DH, Meslet-Cladiere L, Moustafa A, Nehr Z, Nyvall Collén P, Panaud O, Partensky F, Poulain J, Rensing SA, Rousvoal S, Samson G, Symeonidi A, Weissenbach J, Zambounis A, Wincker P, Boyen C. (2013) Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida Proc Natl Acad Sci U S A. 110:5247-5252.
Couradeau E, Benzerara K, Gérard E, Estève I, Moreira D, Tavera R, López-García P. (2013) In situ microscale cyanobacterial calcification in modern microbialites Biogeosciences 10: 5255-5266
López-Pérez M, Gonzaga A, Martin-Cuadrado AB, López-García P, Rodriguez-Valera F, Kimes NE. (2013) Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains Microb Ecol. 65:720-730.
Chevalier N, Bouloubassi I, Birgel D, Taphanel MH, López-García P. (2013) Microbial methane turnover at Marmara Sea cold seeps: a combined 16S rRNA and lipid biomarker investigation Geobiology. 11:55-71.

2012

Lombard J, López-García P, Moreira D. (2012) Phylogenomic investigation of phospholipid synthesis in archaea Archaea. 2012:630910.
Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F. (2012) Polyclonality of concurrent natural populations of Alteromonas macleodii Genome Biol Evol. 4:1360-1374.
Petitjean C, Moreira D, López-García P, Brochier-Armanet C. (2012) Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea BMC Evol Biol. 12:226.
Lombard J, López-García P, Moreira D. (2012) An ACP-independent fatty acid synthesis pathway in archaea: implications for the origin of phospholipids Mol Biol Evol. 29:3261-3265.
Ragon M, Fontaine MC, Moreira D, López-García P. (2012) Different biogeographic patterns of prokaryotes and microbial eukaryotes in epilithic biofilms Mol Ecol. 21:3852-3868.
Lombard J, López-García P, Moreira D. (2012) The early evolution of lipid membranes and the three domains of life Nat Rev Microbiol. 10:507-515.
Couradeau E, Benzerara K, Gérard E, Moreira D, Bernard S, Brown GE Jr, López-García P. (2012) An early-branching microbialite cyanobacterium forms intracellular carbonates Science. 336:459-462.
Bachy C, Gómez F, López-García P, Dolan JR, Moreira D. (2012) Molecular phylogeny of tintinnid ciliates (Tintinnida, Ciliophora) Protist. 163:873-887.
Gómez F, Moreira D, López-García P. (2012) Sinophysis and Pseudophalacroma are distantly related to typical Dinophysoid dinoflagellates (Dinophysales, Dinophyceae) J Eukaryot Microbiol. 59:188-190.
Deschamps P, Moreira D. (2012) Reevaluating the green contribution to diatom genomes Genome Biol Evol. 4:683-688.
López-García P. (2012) The place of viruses in biology in light of the metabolism-versus-replication-first debate Hist. Phil. Life Sci. 34:391-406.
López-García P, Moreira D. (2012) Viruses in biology Evo Edu Outreach. 5:389–398.
Gómez F, Moreira D, Dolan J, López-García P. (2012) Molecular phylogeny of the marine dinoflagellate genus Heterodinium (Dinophyceae) Eur J Phycol. 47:95–104.
Roche SM, Grépinet O, Kerouanton A, Ragon M, Leclercq A, Témoin S, Schaeffer B, Skorski G, Mereghetti L, Le Monnier A, Velge P. (2012) Polyphasic characterization and genetic relatedness of low-virulence and virulent Listeria monocytogenes isolates BMC Microbiol. 12:304.

2011

Couradeau E, Benzerara K, Moreira D, Gérard E, Kaźmierczak J, Tavera R, López-García P. (2011) Prokaryotic and eukaryotic community structure in field and cultured microbialites from the alkaline Lake Alchichica (Mexico) PLoS One. 6:e28767.
Bachy C, López-García P, Vereshchaka A, Moreira D. (2011) Diversity and vertical distribution of microbial eukaryotes in the snow, sea ice and seawater near the north pole at the end of the polar night Front Microbiol. 2:106.
Ragon M, Restoux G, Moreira D, Møller AP, López-García P. (2011) Sunlight-exposed biofilm microbial communities are naturally resistant to Chernobyl ionizing-radiation levels PLoS One. 6:e21764.
Gómez F, López-García P, Moreira D. (2011) Molecular phylogeny of dinophysoid dinoflagellates: the systematic position of Oxyphysis oxytoxoides and the Dinophysis hastata group (Dinophysales, Dinophyceae) J Phycol. 47:393-406.
Brochier-Armanet C, Deschamps P, López-García P, Zivanovic Y, Rodríguez-Valera F, Moreira D. (2011) Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea ISME J. 5:1291-1302.
Deschamps P, Lara E, Marande W, López-García P, Ekelund F, Moreira D. (2011) Phylogenomic analysis of kinetoplastids supports that trypanosomatids arose from within bodonids Mol Biol Evol. 28:53-58
Gómez F, Moreira D, Benzerara K, López-García P. (2011) Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST-3 Environ Microbiol. 13:193-202.
Lara E, Mitchell EA, Moreira D, López García P. (2011) Highly diverse and seasonally dynamic protist community in a pristine peat bog Protist. 162:14-32.
Quaiser A, Zivanovic Y, Moreira D, López-García P. (2011) Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara ISME J. 5:285-304.
Kirkham AR, Jardillier LE, Tiganescu A, Pearman J, Zubkov MV, Scanlan DJ. (2011) Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect Environ Microbiol. 13:975-990.
Gómez F, Moreira D, López-García P. (2011) Avances en el estudio de los dinoflagelados (Dinophyceae) con la filogenia molecular Hidrobiológica, 21:263-284.
Kirkham AR, Jardillier L, Holland R, Zubkov MV, Scanlan DJ. (2011) Analysis of photosynthetic picoeukaryote community structure along an extended Ellett Line transect in the northern North Atlantic reveals a dominance of novel prymnesiophyte and prasinophyte phylotypes Deep Sea Res. Part I. 58:733-744.
Lombard J, Moreira D. (2011) Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life Mol Biol Evol. 28:87-99.
Lombard J, Moreira D. (2011) Early evolution of the biotin-dependent carboxylase family BMC Evol Biol. 11:232.
Stivaletta N, Barbieri R, Cevenini F, López-García P. (2011) Physico-chemical conditions and microbial diversity associated to evaporite deposits in the Laguna de la Piedra (Salar de Atacama, Chile) Geomicrobiol J. 28:83-95.
Kaźmierczak J, Kempe S, Kremer B, López-García P, Moreira D, Tavera R. (2011) Hydrochemistry and microbialites of the alkaline crater Lake Alchichica, Mexico Facies. 57:543-570.
Gómez F, López-García P, Moreira D. (2011) Molecular phylogeny of the sand-dwelling dinoflagellates Amphidiniopsis hirsuta and A. swedmarkii (Peridiniales, Dinophyceae) Acta Protozool. 50:255-262.
Eme L, Trilles A, Moreira D, Brochier-Armanet C. (2011) The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes BMC Evol Biol. 11:265.

2010

Ghai R, Martin-Cuadrado AB, Molto AG, Heredia IG, Cabrera R, Martin J, Verdú M, Deschamps P, Moreira D, López-García P, Mira A, Rodriguez-Valera F. (2010) Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing ISME J. 4:1154-1166
Gómez F, Moreira D, López-García P. (2010) Molecular phylogeny of noctilucoid dinoflagellates (Noctilucales, Dinophyceae) Protist. 161:466-478.
Lara E, Moreira D, López-García P. (2010) The environmental clade LKM11 and Rozella form the deepest branching clade of fungi Protist. 161:116-121.
Gómez F, Moreira D, López-García P. (2010) Neoceratium gen. nov., a new genus for all marine species currently assigned to Ceratium (Dinophyceae) Protist. 161:35-54.
Jardillier L, Zubkov MV, Pearman J, Scanlan DJ. (2010) Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean ISME J. 4:1180-1192.
Colleoni C, Linka M, Deschamps P, Handford MG, Dupree P, Weber AP, Ball SG. (2010) Phylogenetic and biochemical evidence supports the recruitment of an ADP-glucose translocator for the export of photosynthate during plastid endosymbiosis Mol Biol Evol. 27:2691-701.
Gómez F, Moreira D, López-García P. (2010) Molecular phylogeny of the dinoflagellates Podolampas and Blepharocysta (Peridiniales, Dinophyceae) Phycologia. 49:212-220.
Stivaletta N, López-García P, Boihem L, Mille D, Barbieri R. (2010) Biomarkers of endolithic communities within gypsum crusts (Southern Tunisia) Geomicrobiol J. 27:101-110.

2009

Gómez F, López-García P, Moreira D. (2009) Molecular phylogeny of the ocelloid-bearing dinoflagellates Erythropsidinium and Warnowia (warnowiaceae, dinophyceae) J Eukaryot Microbiol. 56:440-445.
Marande W, López-García P, Moreira D. (2009) Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples Environ Microbiol. 11:3179-3188.
Gómez F, López-García P, Nowaczyk A, Moreira D. (2009) The crustacean parasites Ellobiopsis Caullery, 1910 and Thalassomyces Niezabitowski, 1913 form a monophyletic divergent clade within the Alveolata Syst Parasitol. 74:65-74.
Gómez F, Moreira D, López-García P. (2009) Life cycle and molecular phylogeny of the dinoflagellates Chytriodinium and Dissodinium, ectoparasites of copepod eggs Eur J Protistol. 45:260-270.
Gérard E, Moreira D, Philippot P, Van Kranendonk MJ, López-García P. (2009) Modern subsurface bacteria in pristine 2.7 Ga-old fossil stromatolite drillcore samples from the Fortescue Group, Western Australia PLoS One. 4:e5298.
Moreira D, López-García P. (2009) Ten reasons to exclude viruses from the tree of life Nat Rev Microbiol. 7:306-311.
Lara E, Moreira D, Vereshchaka A, López-García P. (2009) Pan-oceanic distribution of new highly diverse clades of deep-sea diplonemids Environ Microbiol. 11:47-55.
Deschamps P, Moreira D. (2009) Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes Mol Biol Evol. 26:2745-2753.
Shi XL, Marie D, Jardillier L, Scanlan DJ, Vaulot D. (2009) Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean PLoS One. 4:e7657.
López-García P, Moreira D. (2009) Yet viruses cannot be included in the tree of life Nature Rev. Microbiol. 7:615–617
Eme L, Moreira D, Talla E, Brochier-Armanet C. (2009) A complex cell division machinery was present in the last common ancestor of eukaryotes PLoS One. 4:e5021.

2008

Quaiser A, López-García P, Zivanovic Y, Henn MR, Rodriguez-Valera F, Moreira D. (2008) Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton Environ Microbiol. 10:2704-2717.
Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P. (2008) Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions ISME J. 2:865-886.
López-García P, Moreira D. (2008) Tracking microbial biodiversity through molecular and genomic ecology Res Microbiol. 159:67-73.
Deschamps P, Colleoni C, Nakamura Y, Suzuki E, Putaux JL, Buléon A, Haebel S, Ritte G, Steup M, Falcón LI, Moreira D, Löffelhardt W, Raj JN, Plancke C, d'Hulst C, Dauvillée D, Ball S. (2008) Metabolic symbiosis and the birth of the plant kingdom Mol Biol Evol. 25:536-548.
Riaz K, Elmerich C, Moreira D, Raffoux A, Dessaux Y, Faure D. (2008) A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases Environ Microbiol. 10:560-570
Moreira D, Brochier-Armanet C. (2008) Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes BMC Evol Biol. 8:12.
Epstein S, López-García P. (2008) Missing protists: a molecular prospective Biodiv Conserv. 17:261-276.

2007

Martín-Cuadrado AB, López-García P, Alba JC, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodríguez-Valera F. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat PLoS One. 2:e914.
Briée C, Moreira D, López-García P. (2007) Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond Res Microbiol. 158:213-227.
López-García P, Vereshchaka A, Moreira D. (2007) Eukaryotic diversity associated with carbonates and fluid-seawater interface in Lost City hydrothermal field Environ Microbiol. 9:546-554.
Moreira D, von der Heyden S, Bass D, López-García P, Chao E, Cavalier-Smith T. (2007) Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata Mol Phylogenet Evol. 44:255-266.
López-Archilla AI, Moreira D, Velasco S, López-García P. (2007) Archaeal and bacterial community composition of a pristine coastal aquifer in Doñana National Park, Spain Aquatic Microbial Ecol. 47:123-139.

2006

Moussard H, Moreira D, Cambon-Bonavita MA, López-García P, Jeanthon C. (2006) Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote FEMS Microbiol Ecol. 57:452-469.
López-García P, Moreira D. (2006) Selective forces for the origin of the eukaryotic nucleus Bioessays. 28:525-533.
Moussard H, Henneke G, Moreira D, Jouffe V, López-García P, Jeanthon C. (2006) Thermophilic lifestyle for an uncultured archaeon from hydrothermal vents: evidence from environmental genomics Appl Environ Microbiol. 72:2268-2271.
Moreira D, Rodríguez-Valera F, López-García P. (2006) Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group Microbiology. 152:505-517.
Slapeta J, López-García P, Moreira D. (2006) Present status of the molecular ecology of kathablepharids Protist. 157:7-11.
Slapeta J, López-García P, Moreira D. (2006) Global dispersal and ancient cryptic species in the smallest marine eukaryotes Mol Biol Evol. 23:23-29.
Benzerara K, Menguy N, López-García P, Yoon TH, Kazmierczak J, Tyliszczak T, Guyot F, Brown GE Jr. (2006) Nanoscale detection of organic signatures in carbonate microbialites Proc Natl Acad Sci U S A. 103:9440-9445.
Benzerara K, Chapon V, Moreira D, López-García P, Heulin T, Guyot F. (2006) Microbial diversity on the Tatahouine meteorite Meteorit. Planet. Sci. 41:1249-1265.
Pascal R, Boiteau L, Forterre P, Gargaud M, Lazcano A, López-García P, Moreira D, Maurel MC, Pereto J, Prieur D, Reisse J. (2006) Prebiotic chemistry - Biochemistry - Emergence of life (4.4-2 Ga) Earth Moon Planets. 98:153-203.
López-García P; Moreira D; Douzery E; Forterre P; Van Zuilen M; Claeys P; Prieur D. (2006) Ancient fossil record and early evolution (ca. 3.8 to 0.5 Ga) Earth Moon Planets. 98:247-290.
Montmerle T, Claeys P, Gargaud M, López-García P, Martin H, Pascal R, Reisse J, Selsis F. (2006) Life on earth ... and elsewhere? Earth Moon Planets. 98:299-312.

2005

Slapeta J, Moreira D, López-García P. (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes Proc Biol Sci. 272:2073-2081.
Bass D, Moreira D, López-García P, Polet S, Chao EE, von der Heyden S, Pawlowski J, Cavalier-Smith T. (2005) Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria Protist. 156:149-161.
Peretó J, López-García P, Moreira D. (2005) Phylogenetic analysis of eukaryotic thiolases suggests multiple proteobacterial origins J Mol Evol. 61:65-74.
López-García P, Kazmierczak J, Benzerara K, Kempe S, Guyot F, Moreira D. (2005) Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey Extremophiles. 9:263-274.
Moreira D, López-García P. (2005) Comment on "The 1.2-megabase genome sequence of Mimivirus" Science. 308:1114.
Nercessian O, Bienvenu N, Moreira D, Prieur D, Jeanthon C. (2005) Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments. Environ. Microbiol 7:118-132.
Gérard E, Guyot F, Philippot P, López-García P. (2005) Fluorescence in situ hybridisation coupled to ultra small immunogold detection to identify prokaryotic cells using transmission and scanning electron microscopy J Microbiol Methods. 63:20-28.
Vickerman K, Appleton PL, Clarke KJ, Moreira D. (2005) Aurigamonas solis n. gen., n. sp., a soil-dwelling predator with unusual helioflagellate organisation and belonging to a novel clade within the Cercozoa Protist. 156:335-354.

2004

Moreira D, López-García P, Vickerman K. (2004) An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea Int J Syst Evol Microbiol. 54:1861-1875.
Moreira D, Ranjard L, López-Garcia P. (2004) The nucleolar proteome and the (endosymbiotic) origin of the nucleus Bioessays. 26:1144-1145.
Peretó J, López-García P, Moreira D. (2004) Ancestral lipid biosynthesis and early membrane evolution Trends Biochem Sci. 29:469-477.
Moreira D, Rodríguez-Valera F, López-García P. (2004) Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes Environ Microbiol. 6:959-969.
López-Archilla AI, Gérard E, Moreira D, López-García P. (2004) Macrofilamentous microbial communities in the metal-rich and acidic River Tinto, Spain FEMS Microbiol Lett. 235:221-228.
Brochier C, López-García P, Moreira D. (2004) Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria Gene. 330:169-176.
López-Archilla AI, Moreira D, López-García P, Guerrero C. (2004) Phytoplankton diversity and cyanobacterial dominance in a hypereutrophic shallow lake with biologically produced alkaline pH Extremophiles. 8:109-115.
López-García P, Brochier C, Moreira D, Rodríguez-Valera F. (2004) Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers Environ Microbiol. 6:19-34.
Glamoclija M, Garrel L, Berthon J, López-García P. (2004) Biosignatures and bacterial diversity in hydrothermal deposits of Solfatara Crater, Italy Geomicrobiol J. 21:529-541.
Danelian T, Moreira D. (2004) Palaeontological and molecular evidence for the origin of silica secreting marine organisms CR Palevol. 3:229-236.
Mira A, Pushker R, Legault BA, Moreira D, Rodríguez-Valera F. (2004) Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics BMC Evol Biol. 4:50.

2003

Moreira D, López-García P. (2003) Are hydrothermal vents oases for parasitic protists? Trends Parasitol. 19:556-558.
López-García P, Duperron S, Philippot P, Foriel J, Susini J, Moreira D. (2003) Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge Environ Microbiol. 5:961-976.
López-García P, Philippe H, Gail F, Moreira D. (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge Proc Natl Acad Sci U S A. 100:697-702.
Bapteste E, Moreira D, Philippe H. (2003) Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase Gene. 318:185-191.

2002

López-García P, Gaill F, Moreira D. (2002) Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila Environ Microbiol. 4:204-215.
Moreira D, López-García P. (2002) The molecular ecology of microbial eukaryotes unveils a hidden world Trends Microbiol. 10:31-38.
López-García P, Rodríguez-Valera F, Moreira D. (2002) Toward the monophyly of Haeckel's radiolaria: 18S rRNA environmental data support the sisterhood of polycystinea and acantharea Mol Biol Evol. 19:118-121.
Brochier C, Bapteste E, Moreira D, Philippe H. (2002) Eubacterial phylogeny based on translational apparatus proteins Trends Genet. 18:1-5.
Moreira D, Kervestin S, Jean-Jean O, Philippe H. (2002) Evolution of eukaryotic translation elongation and termination factors: variations of evolutionary rate and genetic code deviations Mol Biol Evol. 19:189-200.

2001

López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D. (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton Nature. 409:603-607.
Moreira D, López-García P, Rodríguez-Valera F. (2001) New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence Int J Syst Evol Microbiol. 51:2211-2219.
López-García P, López-López A, Moreira D, Rodríguez-Valera F. (2001) Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front FEMS Microbiol Ecol. 36:193-202.
López-García P, Moreira D, López-López A, Rodríguez-Valera F. (2001) A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions Environ Microbiol. 3:72-78.
Moreira D, Philippe H. (2001) Sure facts and open questions about the origin and evolution of photosynthetic plastids Res Microbiol. 152:771-780.

2000

Moreira D, Le Guyader H, Philippe H. (2000) The origin of red algae and the evolution of chloroplasts Nature. 405:69-72.
Philippe H, Lopez P, Brinkmann H, Budin K, Germot A, Laurent J, Moreira D, Müller M, Le Guyader H. (2000) Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions Proc Biol Sci. 267:1213-1221.
Philippe H, Germot A, Moreira D. (2000) The new phylogeny of eukaryotes Curr Opin Genet Dev. 10:596-601.
Brochier C, Philippe H, Moreira D. (2000) The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome Trends Genet. 16:529-533.
Moreira D, Philippe H. (2000) Molecular phylogeny: pitfalls and progress Int Microbiol. 3:9-16.
Myllykallio H, Lopez P, López-García P, Heilig R, Saurin W, Zivanovic Y, Philippe H, Forterre P. (2000) Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon Science. 288:2212-2215.
López-García P, Forterre P. (2000) DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles Bioessays. 22:738-746.

1999

López-García P, Moreira D. (1999) Metabolic symbiosis at the origin of eukaryotes Trends Biochem Sci. 24:88-93.
Moreira D, Philippe H. (1999) Smr: a bacterial and eukaryotic homologue of the C-terminal region of the MutS2 family Trends Biochem Sci. 24:298-300.

1998

Moreira D, López-García P. (1998) Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis J Mol Evol. 47:517-530.