Lipids of marine Archaea: Patterns and provenance in the water-column and sediments

Alonso, 2005, Incorporation of glucose under anoxic conditions by bacterioplankton from coastal North Sea surface waters, Appl. Environ. Microbiol., 71, 1709, 10.1128/AEM.71.4.1709-1716.2005 Alonso, 2006, Concentration-dependent patterns of leucine incorporation by coastal picoplankton, Appl. Environ. Microbiol., 72, 2141, 10.1128/AEM.72.3.2141-2147.2006 Alvarez-Salgado, 2004, Inferring nitrification rates with an inverse method in a coastal upwelling system, Ria de Vigo (NW Spain), Mar. Ecol. Prog. Ser., 276, 3, 10.3354/meps276003 Bano, 2004, Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with antarctic assemblages, Appl. Environ. Microbiol., 70, 781, 10.1128/AEM.70.2.781-789.2004 Beja, 2000, Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage, Environ. Microbiol., 2, 516, 10.1046/j.1462-2920.2000.00133.x Biddle, 2006, Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru, Proc. Natl. Acad. Sci. USA, 103, 3846, 10.1073/pnas.0600035103 Bidigare, 1997, Consistent fractionation of C-13 in nature and in the laboratory: growth-rate effects in some haptophyte algae, Globl Biogeochem. Cycle, 11, 279, 10.1029/96GB03939 Conte, 2001, Seasonal and interannual variability in deep ocean particle fluxes at the Oceanic Flux Program (OFP)/Bermuda Atlantic Time Series (BATS) site in the western Sargasso Sea near Bermuda, Deep-Sea Res. Part II Top. Studies Oceanogr., 48, 1471, 10.1016/S0967-0645(00)00150-8 Conte, 2001, The alkenone temperature signal in western North Atlantic surface waters, Geochim. Cosmochim. Acta, 65, 4275, 10.1016/S0016-7037(01)00718-9 DeLong, 1992, Archaea in Coastal Marine Environments, Proc. Natl. Acad. Sci. USA, 89, 5685, 10.1073/pnas.89.12.5685 DeLong, 2006, Archaeal mysteries of the deep revealed, Proc. Natl. Acad. Sci. USA, 103, 6417, 10.1073/pnas.0602079103 DeLong, 1998, Dibiphytanyl ether lipids in nonthermophilic crenarchaeotes, Appl. Environ. Microbiol., 64, 1133, 10.1128/AEM.64.3.1133-1138.1998 Dumitrescu, 2006, Instability in tropical sea surface temperatures during the Early Aptian, Geology, 34, 833, 10.1130/G22882.1 Francis, 2005, Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean, Proc. Natl. Acad. Sci. USA, 102, 14683, 10.1073/pnas.0506625102 Fuhrman, 1992, Novel major Archaebacterial group from marine plankton, Nature, 356, 148, 10.1038/356148a0 Gattinger, 2002, Phospholipid etherlipid and phospholipid fatty acid fingerprints in selected euryarchaeotal monocultures for taxonomic profiling, FEMS Microbiol. Lett., 213, 133, 10.1111/j.1574-6968.2002.tb11297.x Gibbs, 2006, Shelf and open-ocean calcareous phytoplankton assemblages across the Paleocene-Eocene Thermal Maximum: implications for global productivity gradients, Geology, 34, 233, 10.1130/G22381.1 Goñi, 2003, Biogenic fluxes in the Cariaco Basin: a combined study of sinking particulates and underlying sediments, Deep-Sea Res. Part I Oceanogr. Res. Papers, 50, 781, 10.1016/S0967-0637(03)00060-8 Gowing, 1998, Feeding ecology of the copepod Lucicutia aff. L. grandis near the lower interface of the Arabian Sea oxygen minimum zone, Deep-Sea Res. Part II Top. Studies Oceanogr., 45, 2433, 10.1016/S0967-0645(98)00077-0 Grice, 1998, Isotopically heavy carbon in the C (sub 21) to C (sub 25) regular isoprenoids in halite-rich deposits from the Sdom Formation, Dead Sea Basin, Israel, Org. Geochem., 28, 349, 10.1016/S0146-6380(98)00006-0 Hallam, 2006, Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota, PLoS Biol., 4, e95, 10.1371/journal.pbio.0040095 Herfort, 2006, Application of the TEX86 temperature proxy to the southern North Sea, Org. Geochem., 37, 1715, 10.1016/j.orggeochem.2006.07.021 Herndl, 2005, Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean, Appl. Environ. Microbiol., 71, 2303, 10.1128/AEM.71.5.2303-2309.2005 Hoefs, 1997, Ether lipids of planktonic Archaea in the marine water column, Appl. Environ. Microbiol., 63, 3090, 10.1128/AEM.63.8.3090-3095.1997 Hopmans, 2000, Analysis of intact tetraether lipids in archaeal cell material and sediments by high performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry, Rapid Commun. Mass Spectrom, 14, 585, 10.1002/(SICI)1097-0231(20000415)14:7<585::AID-RCM913>3.0.CO;2-N Huguet C., Kim J.-H., Sinninghe Damsté J. S., and Schouten S. (2006) Reconstruction of sea surface temperature variations in the Arabian Sea over the last 23 kyr using organic proxies (TEX86 and U37K). Paleoceanography 21, PA300310.1029/2005PA001215. Ingalls, 2006, Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon, Proc. Natl. Acad. Sci. USA, 103, 6442, 10.1073/pnas.0510157103 Jenkyns, 2004, High temperatures in the Late Cretaceous Arctic Ocean, Nature, 432, 888, 10.1038/nature03143 Johnson, 2002, A High-Resolution paleoclimate record spanning the past 25,000 years in Southern East Africa, Science, 296, 113, 10.1126/science.1070057 Karner, 2001, Archaeal dominance in the mesopelagic zone of the Pacific Ocean, Nature, 409, 507, 10.1038/35054051 Konneke, 2005, Isolation of an autotrophic ammonia-oxidizing marine archaeon, Nature, 437, 543, 10.1038/nature03911 Langworthy, 1972, Lipids of thermoplasma acidophilum, J. Bacteriol., 112, 1193, 10.1128/JB.112.3.1193-1200.1972 Lee, 1998, Particulate organic carbon fluxes: compilation of results from the 1995 US JGOFS Arabian Sea Process Study, Deep-Sea Res. Part II Top. Studies Oceanogr., 45, 2489, 10.1016/S0967-0645(98)00079-4 Legendre, 1998 Leininger, 2006, Archaea predominate among ammonia-oxidizing prokaryotes in soils, Nature, 442, 806, 10.1038/nature04983 Lopez-Garcia, 2001, A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions, Environ. Microbiol., 3, 72, 10.1046/j.1462-2920.2001.00162.x Macalady, 2004, Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid, Extremophiles, 8, 411, 10.1007/s00792-004-0404-5 Maechler M. (2005) Cluster: Cluster Analysis. R package version 1.10.2. Maindonald, 2003 Massana, 2000, A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces, Appl. Environ. Microbiol., 66, 1777, 10.1128/AEM.66.5.1777-1787.2000 Massana, 1997, Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel, Appl. Environ. Microbiol., 63, 50, 10.1128/AEM.63.1.50-56.1997 Massana, 1998, Vertical distribution and temporal variation of marine planktonic archaea in the Gerlache Strait, Antarctica, during early spring, Limnol. Oceanogr., 43, 607, 10.4319/lo.1998.43.4.0607 McCune, 2002 Menzel, 2006, Membrane tetraether lipids of planktonic Crenarchaeota in Pliocene sapropels of the eastern Mediterranean Sea, Paleogeogr. Paleoclimatol. Paleoecol., 239, 1, 10.1016/j.palaeo.2006.01.002 Minchin, 1987, An evaluation of the relative robustness of techniques for ecological ordination, Vegetatio, 69, 89, 10.1007/BF00038690 Moreira, 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, 10.1111/j.1462-2920.2004.00644.x Murray, 1998, Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica, Appl. Environ. Microbiol., 64, 2585, 10.1128/AEM.64.7.2585-2595.1998 Murray, 1998, Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica, Appl. Environ. Microbiol., 64, 2585, 10.1128/AEM.64.7.2585-2595.1998 Murray, 1999, Evidence for circumpolar distribution of planktonic Archaea in the Southern Ocean, Aquat. Microbiol. Ecol., 18, 263, 10.3354/ame018263 Oksanen J., Kindt R., and O’Hara R. B. (2005) vegan: Community Ecology Package version 1.6-10. <http://cc.oulu.fi/~jarioksa/>. Ouverney, 2000, Marine planktonic Archaea take up amino acids, Appl. Environ. Microbiol., 66, 4829, 10.1128/AEM.66.11.4829-4833.2000 Pancost, 1997, Controls on carbon isotope fractionation by diatoms in the Peru upwelling region, Geochim. Cosmochim. Acta, 61, 4983, 10.1016/S0016-7037(97)00351-7 Pancost, 2003, Carbon isotopic compositions of prokaryotic lipids as tracers of carbon cycling in diverse settings, Chem. Geol., 195, 29, 10.1016/S0009-2541(02)00387-X Pearson, 2001, Origins of lipid biomarkers in Santa Monica Basin surface sediment: a case study using compound-specific Delta C-14 analysis, Geochim. Cosmochim. Acta, 65, 3123, 10.1016/S0016-7037(01)00657-3 Powers, 2005, Large temperature variability in the southern African tropics since the Last Glacial Maximum, Geophys. Res. Lett., 32 Powers, 2004, Crenarchaeotal membrane lipids in lake sediments: a new paleotemperature proxy for continental paleoclimate reconstruction?, Geology, 32, 613, 10.1130/G20434.1 Sambrotto, 2001, Nitrogen production in the northern Arabian Sea during the Spring Intermonsoon and Southwest Monsoon seasons, Deep-Sea Res. Part II Top. Studies Oceanogr., 48, 1173, 10.1016/S0967-0645(00)00135-1 Sambrotto, 2000, Coupling of biological and physical regimes across the Antarctic Polar Front as reflected by nitrogen production and recycling, Deep-Sea Res. Part II Top. Studies Oceanogr., 47, 3339, 10.1016/S0967-0645(00)00071-0 Sarmiento, 2006 Schleper, 1998, Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosium, J. Bacteriol., 180, 5003, 10.1128/JB.180.19.5003-5009.1998 Schleper, 1995, Picrophilus Gen-Nov, Fam-Nov—a novel aerobic, heterotrophic, thermoacidophilic genus and family comprising archaea capable of growth around Ph-0, J. Bacteriol., 177, 7050, 10.1128/jb.177.24.7050-7059.1995 Scholten, 2005, Molecular analysis of the sulfate reducing and archaeal community in a meromictic soda lake (Mono Lake, California) by targeting 16S rRNA, mcrA, apsA, and dsrAB genes, Microbiol. Ecol., 50, 29, 10.1007/s00248-004-0085-8 Schouten, 2003, Extremely high sea-surface temperatures at low latitudes during the middle Cretaceous as revealed by archaeal membrane lipids, Geology, 31, 1069, 10.1130/G19876.1 Schouten, 2000, Widespread occurrence of structurally diverse tetraether membrane lipids: evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles, Proc. Natl. Acad. Sci. USA, 97, 14421, 10.1073/pnas.97.26.14421 Schouten, 2002, Distributional variations in marine crenarchaeotal membrane lipids: a new tool for reconstructing ancient sea water temperatures?, Earth Planet. Sci. Lett., 204, 265, 10.1016/S0012-821X(02)00979-2 Schouten S., Hopmans E. C., Schefuss E., and Sinninghe Damsté J. S. (2003b) Distributional variations in marine crenarchaeotal membrane lipids: a new tool for reconstructing ancient sea water temperatures? (vol. 204, p. 265, 2002). Earth Planet. Sci. Lett. 211, 205–206. Schouten, 2007, Analytical methodology for TEX86 paleothermometry by high-performance liquid chromatography/atmospheric pressure chemical ionization-mass spectrometry, Anal. Chem., 79, 2940, 10.1021/ac062339v Schouten, 2001, Evidence for anaerobic methane oxidation by archaea in euxinic waters of the Black Sea, Org. Geochem., 32, 1277, 10.1016/S0146-6380(01)00110-3 Shimada, 2002, Complete polar lipid composition of Thermoplasma acidophilum HO-62 determined by high-performance liquid chromatography with evaporative light-scattering detection, J. Bacteriol., 184, 556, 10.1128/JB.184.2.556-563.2002 Sinninghe Damsté, 2002, Distribution of membrane lipids of planktonic Crenarchaeota in the Arabian sea, Appl. Environ. Microbiol., 68, 2997, 10.1128/AEM.68.6.2997-3002.2002 Sinninghe Damsté, 1997, Is there evidence for a substantial contribution of prokaryotic biomass to organic carbon in Phanerozoic carbonaceous sediments?, Org. Geochem., 26, 517, 10.1016/S0146-6380(97)00039-9 Sluijs, 2006, Subtropical arctic ocean temperatures during the Palaeocene/Eocene thermal maximum, Nature, 441, 610, 10.1038/nature04668 Smittenberg, 2004, Compound-specific radiocarbon dating of the varved Holocene sedimentary record of Saanich Inlet, Canada, Paleoceanography, 19 Swain, 1997, Identification of beta-l-gulose as the sugar moiety of the main polar lipid Thermoplasma acidophilum, Biochim. Biophys. Acta Lipids Lipid Metab., 1345, 56, 10.1016/S0005-2760(96)00163-4 Taylor, 2003, Temporal variations in viral distributions in the anoxic Cariaco Basin, Aquat. Microb. Ecol., 30, 103, 10.3354/ame030103 Thunell, 2000, Organic carbon fluxes, degradation, and accumulation in an anoxic basin: sediment trap results from the Cariaco Basin, Limnol. Oceanogr., 45, 300, 10.4319/lo.2000.45.2.0300 Wakeham, 1997, Compositions and transport of lipid biomarkers through the water column and surficial sediments of the equatorial Pacific Ocean, Deep-Sea Res. Part II–Top. Studies Oceanogr., 44, 2131, 10.1016/S0967-0645(97)00035-0 Wakeham, 2004, Archaeal lipids and anaerobic oxidation of methane in euxinic water columns: a comparative study of the Black Sea and Cariaco Basin, Chem. Geol., 205, 427, 10.1016/j.chemgeo.2003.12.024 Wakeham, 2003, Archaea mediate anaerobic oxidation of methane in deep euxinic waters of the Black Sea, Geochim. Cosmochim. Acta, 67, 1359, 10.1016/S0016-7037(02)01220-6 Wakeham, 2002, Lipid biomarker fluxes in the Arabian Sea, with a comparison to the equatorial Pacific Ocean, Deep-Sea Res. Part II Top. Studies Oceanogr., 49, 2265, 10.1016/S0967-0645(02)00037-1 Wassmann, 2000, Vertical flux of faecal pellets and microplankton on the shelf of the oligotrophic Cretan Sea (NE Mediterranean Sea), Prog. Oceanogr., 46, 241, 10.1016/S0079-6611(00)00021-5 Weijers, 2006, Membrane lipids of mesophilic anaerobic bacteria thriving in peats have typical archaeal traits, Environ. Microbiol., 8, 648, 10.1111/j.1462-2920.2005.00941.x Wishner, 1998, Mesozooplankton biomass in the upper 1000m in the Arabian Sea: overall seasonal and geographic patterns, and relationship to oxygen gradients, Deep-Sea Res. Part II Top. Studies Oceanogr., 45, 2405, 10.1016/S0967-0645(98)00078-2 Wuchter C., Abbas B., Coolen M. J. L., Herfort L., van Bleijswijk J., Timmers P., Strous M., Teira E., Herndl G. J., Middelburg J. J., Schouten S., and Sinninghe Damsté J. S. (2006a) Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. USA 103, 12317–12322, 10.1073/pnas.0600756103. Wuchter, 2006, Archaeal tetraether membrane lipid fluxes in the northeastern Pacific and the Arabian Sea: implications for TEX86 paleothermometry, Paleoceanography, 21 Wuchter, 2005, Temporal and spatial variation in tetraether membrane lipids of marine Crenarchaeota in particulate organic matter: implications for TEX86 paleothermometry, Paleoceanography, 20 Wuchter, 2004, Temperature-dependent variation in the distribution of tetraether membrane lipids of marine Crenarchaeota: implications for TEX86 paleothermometry, Paleoceanography, 19 Wuchter, 2003, Bicarbonate uptake by marine Crenarchaeota, FEMS Microbiol. Lett., 219, 203, 10.1016/S0378-1097(03)00060-0 Zachos, 2006, Extreme warming of mid-latitude coastal ocean during the Paleocen-Eocene thermal maximum: inferences from TEX86 and isotope data, Geology, 34, 737, 10.1130/G22522.1