Program 1050
The role of crenarchaeota in the marine nitrogen cycleProgram coordinator(s):
Prof. dr. J. S. Sinninghe DamstéTheme(s):
1 Funding date: 11-jan-06
AbstractPlanktonic archaea form one of the most abundant groups of unicellular organisms in today’s oceans and comprise up to 20% of prokaryotic cells. However, their role in the marine biogeochemical cycles remained enigmatic. Recent evidence suggests that they may be involved in the N-cycle. We have recently enriched a marine Crenarchaeote that oxidizes ammonia to nitrite. Field studies in the North Sea show that abundance of these Crenarchaeota and their ammonia monooxygenase genes strongly increase in autumn with strongly declining ammonia and increasing nitrite and nitrate levels. This suggests a crucial role for these archaea in the biogeochemical N-cycle.
In this program we want to study the importance of marine Crenarchaeota in marine nitrification. To this end, we will isolate marine Crenarchaeota and study their physiology and lipid chemistry. Field studies will be undertaken in coastal seas and the open ocean to examine the relative importance of archaeal versus bacterial nitrification using state of the art molecular biological techniques, 15N and 13C labeling and lipid analysis. Finally, we will examine the potential of crenarchaeotal lipids to trace past nitrification rates. The result of this program will lead to new insights into the microbial roots of the global marine N-cycle.
This program contains the following projects:1051: Ecophysiology and role of marine crenarchaeota in the present day marine N cycle1052: Biogeochemistry of archaeal and bacterial nitrification in coastal ecosystems1053: Ecology and lipid chemistry of marine Crenarchaeota in present and past marine environmentsPublicationsHaaijer, S.C.M., Lamers, L.P.M., Smolders, A.J.P., Jetten, M.S.M., Op de Camp, H.J.M., 2007
(2007). Iron sulfide and pyrite as potential electron donors for microbial nitrate reduction in freshwater wetlands
. Geomicrobiology Journal24 (5): 391-401.
Darwin Center authors: op den Camp H. J. M., Haaijer S. C. M., Jetten M. S. M.Cook, P.L.M., Veuger, B., Böer, S., Middelburg, J.J.
(2007). Effect of nutrient availability on carbon and nitrogen incorporation and flows through benthic algae and bacteria in near-shore sandy sediment
. Aquatic Microbial Ecology49: 165-180.
Darwin Center authors: Middelburg J.J., Veuger B.Veuger, B., Eyre, B.D., Maher, D., Middelburg, J.J.
(2007). Nitrogen incorporation and retention by bacteria, algae, and fauna in a subtropical intertidal sediment: An in situ 15N-labeling study
. Limnology and Oceanography52 (5): 1930-1942.
Darwin Center authors: Middelburg J.J., Veuger B.Teugels, B., Bouillon, S., Veuger, B., Middelburg, J.J., Koedam, N. (2008). Kleptoplasts mediate nitrogen acquisition in the sea slug Elysia viridis.
Darwin Center authors: Middelburg J.J., Veuger B.Haaijer, S.C.M., Harhangi, H.R., Meijerink, B.B., Strous, M., Pol, A., Smolders, A.J.P., Verwegen, K., (...), Op Den Camp, H.J.M.
(2008). Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem
. ISME2 (12): 1231-1242.
Darwin Center authors: op den Camp H. J. M., Haaijer S. C. M.Evrard, V., Cook, P.L.M., Veuger, B., Huettel, M., Middelburg, J.J.
(2008). Tracing carbon and nitrogen incorporation and pathways in the microbial community of a photic subtidal sand
. Aquatic Microbial Ecology53 (3): 257-269.
Darwin Center authors: Middelburg J.J., Veuger B.Pitcher, A., Schouten, S., Sinninghe Damsté, J.S.
(2009). In situ production of crenarchaeol in two California hot springs
. Applied and Environmental Microbiology75 (13): 4443-4451.
Darwin Center authors: Pitcher A., Schouten S., Sinninghe Damsté J. S.Pitcher, A., Hopmans, E.C., Schouten, S., Sinninghe Damsté, J.S.
(2009). Separation of core and intact polar archaeal tetraether lipids using silica columns: Insights into living and fossil biomass contributions
. Organic Geochemistry40 (1): 12-19.
Darwin Center authors: Hopmans E. C., Pitcher A., Schouten S., Sinninghe Damsté J. S.Gribsholt, B., Veuger, B., Tramper, A., Middelburg, J.J., Boschker, H.T.S.
(2009). Long-term 15N-nitrogen retention in tidal freshwater marsh sediment: Elucidating the microbial contribution
. Limnology and Oceanography54 (1): 13-22.
Darwin Center authors: Boschker H. T. S., Middelburg J.J., Veuger B.Jia Yan, Op den Camp, H.J.M., Jetten, M.S.M., Yong Y. Hu, and Haaijer, S.C.M. (2010). Induced cooperation between marine nitrifiers and anaerobic ammonium-oxidizing bacteria by incremental exposure to oxygen. Systematic and Applied Microbiologydoi:10.1016/j.syapm.2010.08.003:
Darwin Center authors: op den Camp H. J. M., Haaijer S. C. M., Jetten M. S. M.Pitcher A., Rychlik N., Hopmans E.C., Spieck E., Rijpstra I.C., Ossebaar J., Wagner M., Schouten S., Sinninghe Damsté J.S. (2010). Crenarchaeol dominates the membrane lipids of "Candidatus Nitrososphaera gargensis", a thermophilic Group I.1b Archaeon. ISME Journal542-552.
Darwin Center authors: Hopmans E. C., Pitcher A., Schouten S., Sinninghe Damsté J. S.Hardison AK, Canuel EA, Anderson IC, Veuger B. (2010). Fate of macroalgae in benthic systems: Carbon and nitrogen cycling within the microbial community. Marine Ecology Progress Series414: 41-55.
Darwin Center authors: Veuger B.A.M. Pitcher (2011). Intact polar lipids of ammonia-oxidizing Archaea: Structural diversity and application in
molecular ecology.
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Darwin Center authors: Pitcher A.Pitcher, A., Hopmans, E.C., Mosier, A.C., Park, S.J., Rhee, S-.K., Francis, C.A., Schouten, S., Sinninghe Damsté, J.S. (2011). Core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing Archaea enriched from marine and estuarine sediments.. Appl. Env. Microbiol.77: 3468-3477.
Darwin Center authors: Hopmans E. C., Pitcher A., Schouten S., Sinninghe Damsté J. S.M. Mußmann, I. Brito, A. Pitcher, J.S. Sinninghe Damsté, R. Hatzenpichler, A. Richter, J.L. Nielsen, P.H. Nielsen, A. Müller, H. Daims, M. Wagner, I.M Head (2011). Abundant activated sludge thaumarchaeotes express amoA but do not live primarily from autotrophic ammonia oxidation.. PNAS108: 16771-16776.
Darwin Center authors: Pitcher A., Sinninghe Damsté J. S.Pitcher, A., Villanueva, L., Hopmans, E.C. , Schouten, S., Reichart, G.-J., Sinninghe Damsté, J.S.
(2011). Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone
. ISME JournalVolume 5, Issue 12: 1896-1904.
Darwin Center authors: Hopmans E. C., Pitcher A., Reichart G. J., Schouten S., Sinninghe Damsté J. S., Villanueva L.Bart Veuger and Dick van Oevelen (2011). Long-term pigment dynamics and diatom survival in dark sediment. Limnology and OceanographyVolume 56, Issue 3: 1065-1074.
Darwin Center authors: Veuger B.Pitcher A., Hopmans E.C., Mosier A.C., Park S.J., Rhee S-.K., Francis C.A., Schouten S., Sinninghe Damsté J.S. (2011). Core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing Archaea enriched from marine and estuarine sediments.. Applied and Environmental Microbiology77: 3468-3477.
Darwin Center authors: van Boxel J. H., Hopmans E. C., Pitcher A., Schouten S., Sinninghe Damsté J. S.William R. Hunter, Bart Veuger and Ursula Witte (2012). Macrofauna regulate heterotrophic bacterial carbon and nitrogen incorporation in low-oxygen sediments. The ISME Journal1-12:
Darwin Center authors: Veuger B.Tierney, J.E., Schouten, S., Pitcher, A., Hopmans, E.C., Sinninghe Damsté, J.S. (2012). Core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs) in Sand Pond, Warwick, Rhode Island (USA): Insights into the origin of lacustrine GDGTs. Geochimica et Cosmochimica Acta77: 561-581.
Darwin Center authors: Hopmans E. C., Pitcher A., Schouten S., Sinninghe Damsté J. S.Haaijer SCM, Crienen G, Jetten MSM , Op den Camp HJM (2012). Anoxic iron cycle bacteria from an iron sulfide- and nitrate-rich freshwater environment. Front. Microbiol.3:
Darwin Center authors: op den Camp H. J. M., Haaijer S. C. M., Jetten M. S. M.Tom Van Engeland, Tjeerd J. Bouma, Edward P. Morris, Fernando G. Brun, Gloria Peralta, Miguel Lara, Iris E. Hendriks, Pieter van Rijswijk, Bart Veuger, Karline Soetaert, Jack J. Middelburg (2013). Dissolved organic matter uptake in a temperate
seagrass ecosystem. MARINE ECOLOGY PROGRESS SERIES478: 87-100.
Darwin Center authors: Middelburg J.J., Soetaert K. E. R., Veuger B.Veuger, B., Pitcher, A., Schouten, S., Sinninghe Damsté, J.S., Middelburg, J.J. (2013). Nitrification and growth of autotrophic nitrifying bacteria and Thaumarchaeota in the coastal North Sea..
Darwin Center authors: Middelburg J.J., Pitcher A., Schouten S., Sinninghe Damsté J. S., Veuger B.