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Pu­bli­ka­tio­nen 2004

Pu­bli­ka­tio­nen 2004

De­part­ment of Bio­geo­che­mis­try

Böning, H.P., Brumsack H.-J., Böttcher M.E., Schnetger B., Kriete C., Kallmeyer J. & Borchers S.L.: Geo­che­mis­try of Pe­ru­vi­an near-sur­face se­di­ments. Geochim. Cos­mochim. Acta 68(21):4429-4451 (2004).  ScienceDirect
Böttcher , M.E., Hespenheide B., Brumsack H.-J. & Bosselmann K.: Sta­ble iso­to­pe bio­geo­che­mis­try of the sul­fur cy­cle in mo­dern ma­ri­ne se­di­ments: I. Sea­so­nal dy­na­mics in a tem­pe­ra­te in­terti­dal san­dy sur­face se­di­ment. Iso­topes En­vi­ron. Health Stud. 40(4):267-283 (2004).  PubMed
Böttcher, M.E. & Schnetger B.: Chap­ter 27. Di­rect mea­su­re­ment of the con­tent and iso­to­pic com­po­si­ti­on of sul­fur in black shales by me­ans of com­bus­ti­on-iso­to­pe-ra­tio-mo­ni­to­ring mass spec­tro­me­try (C-irmMS). Hand­book of Sta­ble Iso­to­pe Ana­ly­ti­cal Tech­ni­ques, Vol. I (P. de Groot, ed.), El­se­vier, pp.597-603 + 2pp. Re­fe­ren­ces (2004).
Böttcher, M.E., Khim B.-K., Suzuki A., Gehre M., Wortmann U.G. & Brumsack H.-J.: Mi­cro­bi­al sul­fa­te re­duc­tion in deep se­di­ments of the sou­thwest Pa­ci­fic (ODP Leg 181, Sites 1119 to 1125): Evi­dence from sta­ble sul­fur iso­topes frac­tio­na­ti­on and pore wa­ter mo­de­ling. Mar. Geol. 205:249-260 (2004).  ScienceDirect
Butler, I.B., Böttcher M.E., Rickard D. & Olroyd A.: Sul­fur iso­to­pe par­ti­tio­n­ing du­ring ex­pe­ri­men­tal for­ma­ti­on of py­ri­te via the po­lys­ul­fi­de and hy­dro­gen sul­fi­de pa­thways: Im­pli­ca­ti­ons for the in­ter­pre­ta­ti­on of se­di­men­ta­ry and hydro­ther­mal py­ri­te iso­to­pe re­cor­ds. Earth Pla­net. Sci. Lett. 228:495-509 (2004).  ScienceDirect
D′Hondt, S.D., Jørgensen, B.B., Miller, D.J., Batzke, A., Blake, R., Cragg, B.A., Cypionka, H., Dickens, G.R., Ferdelman, T., Hinrichs, K.-H., Holm, N.G., Mitterer, R., Spivack, A., Wang, G., Bekins, B., Engelen, B., Ford, K., Gettemy, G., Rutherford, S.D., Sass, H., Skilbeck, C.G., Aiello, I.W., Guèrin, G., House, C.H., Inagaki, F., Meister, P., Naehr, T., Niitsuma, S., Parkes, R.J., Schippers, A., Smith, D.C., Teske, A., Wiegel, J., Naranjo Padilla, C., Solis Acosta, J.L.: Dis­tri­bu­ti­ons of mi­cro­bi­al ac­tivi­ties in deep sub­seaf­loor se­di­ments. Sci­ence 306:2216-2221 (2004).  PubMed  Full Text
Emeis, K-C., Brüchert, V., Currie, B., Endler, R., Ferdelman, T., Kiessling, A., Leipe, T., Noli-Peard, K., Struck, U. and Vogt, T.: Shal­low gas in shelf se­di­ments of the Na­mi­bi­an Co­as­tal Up­wel­ling Eco­sys­tem. Cont. Shelf Res., 24:627-642 (2004).  ScienceDirect
Jørgensen, B. B., Böttcher, M. E., Lüschen, H., Neretin, L. N. and Volkov, I.I.: An­ae­ro­bic me­tha­ne oxi­da­ti­on and a deep H2S sink ge­ne­ra­te iso­to­pi­cal­ly hea­vy sul­fi­des in Black Sea se­di­ments. Geochi­mi­ca et Cos­mochi­mi­ca Acta, 68(9):2095-2118 (2004).  ScienceDirect
Jørgensen, B. B. & D. C. Nelson: Sul­fi­de oxi­da­ti­on in ma­ri­ne se­di­ments: Geo­che­mis­try meets mi­cro­bio­lo­gy, pp. 63-81. In Sul­fur Bio­geo­che­mis­try – Past and Pre­sent., J. P. Amend, K. J. Ed­wards, and T. W. Ly­ons (eds.), Geo­lo­gi­cal So­cie­ty of Ame­ri­ca, Spe­cial Pa­per 379 (2004).  GSA
Kallmeyer, J., Ferdelman, T. G., Weber, A., H. Fossing & B. B. Jørgensen: A cold chro­mi­um di­stil­la­ti­on pro­ce­du­re for ra­diola­be­led sul­fi­de ap­p­lied to sul­fa­te re­duc­tion mea­su­re­ments. Lim­no­lo­gy and Ocea­no­gra­phy: Me­thods, 2: 171-180 (2004). Full Text
Kallmeyer, J. and Boetius, A.: Ef­fects of tem­pe­ra­tu­re and pres­su­re on sul­fa­te re­duc­tion and an­ae­ro­bic oxi­da­ti­on of me­tha­ne in hydro­ther­mal se­di­ments of Gu­ay­mas Ba­sin. Ap­p­lied and En­vi­ron­men­tal Mi­cro­bio­lo­gy, 70(2):1231-1233 (2004).  PubMed  Full Text
Kolb, J., Hellmann A., Rogers A., Sindern S., Vennemann T.W., Böttcher M.E. & Meyer F.M.: The role of a tran­scru­s­tal she­ar zone in oro­ge­nic gold mi­ne­ra­liza­t­i­on at the Ajja­nah­al­li mine, Dhar­war Cra­ton, South In­dia. Econ. Geol. 99:743-759 (2004).  GeoSci
Kuypers, M.M.M., Van Breugel, Y., Schouten, S., Erba, E., Sinninghe Damsté, J. S.: N2-fi­xing cya­no­bac­te­ria sup­p­lied nut­ri­ent N for Cret­aceous ocea­nic an­oxic events. Geo­lo­gy, 32(10):853-856 (2004).  Geology
Kuypers, M. M. M., Lourens L. J., Rijpstra W. F. C., Pancost R. D., Nijenhuis I. A., and Damsté J. S. S.: Or­bi­tal for­cing of or­ga­nic car­bon bu­ri­al in the pro­to-North At­lan­tic du­ring ocea­nic an­oxic event 2. Earth and Pla­ne­ta­ry Sci­ence Let­ters 228(3-4):465-482 (2004).  ScienceDirect
Mienert, J., P. P. E. Weaver, S. Berné, W. C. Dullo, D. Evans, A. Freiwald, J.-P. Henriet, B. B. Jørgensen, G. Lericolais, V. Lykousis, J. Parkes, F. Trincardi and G. Westbrook: Over­view of re­cent, on­go­ing, and fu­ture in­ves­ti­ga­ti­ons on the dy­na­mics and evo­lu­ti­on of Eu­ro­pean mar­gins. Ocea­no­gra­phy, 17(4):16-33 (2004).  Oceanography  Full Text
Neretin, L. N., M. E. Böttcher, B. B. Jørgensen, I. I. Volkov, H. Lüschen & K. Hilgenfeldt: Py­ri­tiza­t­i­on pro­ces­ses and grei­gi­te for­ma­ti­on in the ad­van­cing sul­fi­di­za­t­i­on front in the up­per Plei­sto­ce­ne se­di­ments of the Black Sea. Geochi­mi­ca et Cos­mochi­mi­ca Acta, 68(9):081-2093 (2004).  ScienceDirect
Schmid, M.C., Maas B., Dapena A., van de Pas-Schoonen K., van de Vossenberg J., Kartal B., van Niftrik L., Schmidt I., Cirpus I., Kuenen J. G., Wagner M., Damsté J. S. S., Kuypers M., Revsbech N. P., Mendez R., Jetten M. S. M., and Strous M.: Bio­mar­kers for in situ de­tec­tion of an­ae­ro­bic am­mo­ni­um-oxi­di­zing (anam­m­ox) bac­te­ria. Ap­p­lied and En­vi­ron­men­tal Mi­cro­bio­lo­gy 71(4):1677-1684 (2005).  PubMed  Full Text
Schouten, S., Strous M., Kuypers M. M. M., Rijpstra W. I. C., Baas M., Schubert C. J., Jetten M. S. M., and Damste J. S. S.: Sta­ble car­bon iso­to­pic Frac­tio­na­ti­ons as­so­cia­ted with in­or­ga­nic car­bon fixa­ti­on by an­ae­ro­bic am­mo­ni­um-oxi­di­zing bac­te­ria. Ap­p­lied and En­vi­ron­men­tal Mi­cro­bio­lo­gy 70(6):3785-3788 (2004).  PubMed  Full Text
Zopfi, J, T. Ferdelman and H. Fossing: Dis­tri­bu­ti­on and fate of sul­fur in­ter­me­dia­tes – sul­fi­te, te­tra­thio­na­te, thio­sul­fa­te, and ele­men­tal sul­fur – in ma­ri­ne se­di­ments. GSA Spe­cial Pa­pers 379:97-116 (2004).  GSA
Diploma theses
Peters, Lydia: Zur Bio­geo­che­mis­try ei­nes Se­di­ment­ker­nes aus dem Mischwatt der süd­li­chen Nord­see (2004).
Theune, Alexandra: Bio­geo­che­mi­sche Pro­zes­se im Koh­len­stoff-, Ei­sen-, Man­gan- und Schwe­fel­kreis­lauf in­terti­da­ler Se­di­men­te der süd­li­chen Nord­see (2004).

De­part­ment of Mi­cro­bio­lo­gy

Detmers, J., Strauss, H., Schulte, U., Bergmann, A., Knittel, K., Kuever, J.: FISH shows that Desulfotomaculum spp. are the do­mi­na­ting sul­fa­te-re­du­cing bac­te­ria in a pris­ti­ne aqui­fer. Mi­cro­bi­al Eco­lo­gy, 47:236-242 (2004).  PubMed
Dinh, H.T., Kuever, J., Mußmann, M., Hassel, A. W., Stratmann, M., Widdel, F.: Iron cor­ro­si­on by no­vel an­ae­ro­bic mi­cro­or­ga­nisms. Na­tu­re 427:829-832 (2004).  PubMed
Gade, D., H. Schlesner, F. O. Glöckner, R. Amann, S. Pfeiffer, and M. Thomm: Iden­ti­fi­ca­ti­on of planc­to­my­ce­tes with or­der-, ge­nus- and strain-spe­ci­fic 16S rRNA-tar­ge­ted pro­bes. Mi­cro­bio­lo­gy Eco­lo­gy 47:243-251 (2004).  PubMed
Grünberg, K., E. C. Müller, A. Otto, R. Reszka, D. Linder, M. Kube, R. Reinhardt, and D. Schüler: Bio­che­mi­cal and pro­teo­mic ana­ly­sis of the ma­gne­to­so­me mem­bra­ne in Magnetospirillum gryphiswaldense. Appl. Ev­i­ron. Mi­cro­bi­ol. 70(2):1040-1050 (2004).  PubMed  Full Text
Hai, T., Lange D., Rabus R., Steinbüchel A.: Po­ly­hy­droxyal­ka­noa­te (PHA) ac­cu­mu­la­ti­on in sul­fa­te-re­du­cing bac­te­ria and iden­ti­fi­ca­ti­on of a class-III PHA syn­tha­se (Pha­EC) in Desulfococcus multivorans. Appl En­vi­ron Mi­cro­bi­ol 70(8):4440-4448 (2004).  PubMed  Full Text
Handrick, R., S. Reinhardt, D. Schultheiss, T. Reichart, D. Schüler, V. Jendrossek, and D. Jendrossek: Un­ra­ve­ling the func­tion of the Rhodospirillum rubrum ac­tiva­tor of po­ly­hy­droxy­bu­ty­ra­te (PHB) de­gra­da­ti­on: the ac­tiva­tor is a PHB-gra­nu­le-bound pro­te­in (pha­sin). J. Bac­te­ri­ol. 186(8):2466-75 (2004).  PubMed  Full Text
Hoell, A., A. Wiedenmann, U. Heyen, and D. Schüler: Na­no­struc­tu­re and field-in­du­ced ar­ran­ge­ment of ma­gne­to­so­mes stu­di­ed by SANS­POL. Phy­si­ca B: Con­den­s­ed Mat­ter 350:e309-e313 (2004).  ScienceDirect
Hufnagel, P., Schweiger-Hufnagel U., Behrens M., Macht M., Baessmann C., Suckau D., Schürenberg M., Rabus R.: Bak­te­ri­um mit vor­her­ge­sag­ten ORFs – eine Her­aus­for­de­rung für die Pro­teom­ana­ly­tik. La­bor­welt 5(4):31-34 (2004).
Kube, M., Heider J., Amann J., Hufnagel P., Kühner S., Beck A., Reinhardt R., Rabus R.: Ge­nes in­vol­ved in the an­ae­ro­bic de­gra­da­ti­on of to­lue­ne in a de­ni­tri­fy­ing bac­te­ri­um, strain EbN1. Arch Mi­cro­bi­ol 181:182-194 (2004).  PubMed
Musat, F., Wieland, A., Widdel, F.: Ma­ri­ne se­di­ment with sur­face con­ta­mi­na­ti­on by oil in mi­cro­cosms for mi­cro­bio­lo­gi­cal stu­dies. Ophe­lia 58 (3):217-222 (2004).  TFO
Rabus, R., Ruepp A., Frickey T., Rattei T., Fartmann B., Stark M., Bauer M., Zibat A., Lombardot T., Becker I., Amann J., Gellner K., Reeling H., Leuschner W.D., Glöckner F.-O., Lupas A.N., Amann R., Klenk H.-P.: The ge­no­me of Desulfotalea psychrophila, a sulp­ha­te-re­du­cing bac­te­ri­um from per­man­ent­ly cold Arc­tic se­di­ments. En­vi­onmen­tal Mi­cro­bio­lo­gy, 6(9):887-902 (2004).  PubMed
Rehm, B., and D. Schüler: Klein–Klei­ner–Am Kleins­ten: Na­no­bio­tech­no­lo­gie, eine Schlüs­sel­tech­no­lo­gie des 21. Jahr­hun­derts, pp.56-61, In: Bio­tech­no­lo­gie 2020. DE­CHE­MA, Frank­furt (2004).  UO
Schlesner, H, Rensmann C, Tindall B J, Gade D, Rabus R, Pfeiffer S, Hirsch P: Ta­xo­no­mic he­te­ro­gen­ei­ty wi­t­hin the Planctomycetales as de­ri­ved by DNA-DNA hy­bri­di­za­t­i­on, de­scrip­ti­on of Rhodopirellula baltica gen. nov., sp. nov. and trans­fer of Pirellula marina to the ge­nus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emen­ded de­scrip­ti­on of the ge­nus Pirellula. Int. J. Syst. Evol. Mi­cro­bi­ol. 54:1567-1580 (2004).  PubMed  Full Text
Schüler, D.: Chap­ter 4. Bio­che­mi­cal and ge­ne­tic ana­ly­sis of the ma­gne­to­so­me mem­bra­ne in Magnetospirillum gryphiswaldense. pp.61-73, In Bio­mi­ne­ra­liza­t­i­on. 2nd ed., E. Bäu­er­lein (ed.), Wi­ley-VCH, Wein­heim, Ger­ma­ny (2004).  PubMed  Full Text
Schüler, D.:  Mole­cu­lar ana­ly­sis of a sub­cel­lu­lar com­part­ment: The ma­gne­to­so­me mem­bra­ne in Magnetospirillum gryphiswaldense. Arch. Mi­cro­bi­ol. 181:1-7 (2004).  PubMed
Schweiger-Hufnagel, U., Behrens M., Jürgens M., Baessmann C., Suckau D., Rabus R.: Neu­es Werk­zeug für die de-novo Se­quen­zie­rung von Pro­te­inen. Bio­spek­trum Son­der­aus­ga­be 10. Jahr­gang, 566-567 (2004). Full Text
Widdel, F., Boetius, A., Rabus, R.: An­ae­ro­bic bio­de­gra­da­ti­on of hy­dro­c­ar­bons in­clu­ding me­tha­ne. In The Pro­ka­ryo­tes, elec­tro­nic edi­ti­on. Dwor­kin, M., Fal­kow, S., Ro­sen­berg, E., Schlei­fer, K.-H., Sta­cke­brandt, E. (eds), Sprin­ger, New York (2004).  Springer
Zhilina, T.N., Appel, R., Probian, C., Llobet Brossa, E., Harder, J., Widdel, F., Zavarzin, G.A.: Alkaliflexus imshenetskii gen. nov. sp. nov., a new al­ka­li­phi­lic gli­ding car­bo­hy­dra­te-fer­men­ting bac­te­ri­um with pro­pio­na­te for­ma­ti­on from a soda lake. Arch. Mi­cro­bi­ol. 182: 244-253 (2004).  PubMed
Diploma theses
Gärdes, Astrid: De­le­ti­ons­mu­ta­ge­ne­se ei­nes Ma­gne­to­so­men­pro­te­ins in Magnetospirillum gryphiswaldense un­ter Eta­blie­rung des Cre-loxP-Sys­tems. Di­plom­ar­beit. Fach­hoch­schu­le Em­den (2004).
Ullrich, Susanne: Un­ter­su­chun­gen zur Ge­ne­tik und Mu­ta­bi­li­tät der Ma­gne­to­so­men­in­sel von Magnetospirillum gryphiswaldense MSR-1. Di­plom­ar­beit. Uni­ver­si­tät Bre­men (2004)
Ph.D. theses
Amann, Judith: Me­ta­bo­li­sche Re­gu­la­ti­on und Re­kon­struk­ti­on bei Desulfobacterium  autotrophicum. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 161pp.
Flies, Christine: Iso­lie­rung und ku­li­vie­rungs­un­ab­hän­gi­ge Un­ter­su­chun­gen von ma­gne­to­tak­ti­schen Bak­te­ri­en aus ma­ri­nen und lim­ni­schen Se­di­men­ten. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004) 176pp.
Gade, Dörte: Phy­sio­lo­gi­sche und pro­teo­mi­sche Un­ter­su­chun­gen am ma­ri­nen Plank­to­my­ce­ten Rhodopirellula baltica.  Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 223pp.
Schultheiss, Daniel: Ent­wick­lung ei­nes ge­ne­ti­schen Sys­tems für die Un­ter­su­chung der Ma­gne­tit­bio­mi­ne­ra­li­sa­ti­on bei dem ma­gne­ti­schen Bak­te­ri­um  Magnetospirillum gryphiswaldense MSR-1. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 186pp.
Habilitation
Dirk Schüler: Ha­bi­li­ta­ti­on, Uni­ver­si­tät Bre­men, Bre­men (2004).

Mole­cu­lar Eco­lo­gy Group

Amann, R., R. Rosselló-Mora, C. Flies, and D. Schüler: Chap­ter 3. Phy­lo­ge­ny and in situ iden­ti­fi­ca­ti­on of ma­gne­tot­ac­tic bac­te­ria. p. 45-60,  In: Bio­mi­ne­ra­liza­t­i­on (2nd Edi­ti­on), E. Bäu­er­lein (Ed.), Wi­ley-VCH, Wein­heim, Ger­ma­ny (2004).Wiley
Behrens, S., Fuchs B. M. , and R. Amann: The ef­fect of nu­cle­o­ba­se-spe­ci­fic fluo­re­scence quen­ching on in situ hy­bri­di­za­t­i­on with rRNA-tar­ge­ted oli­go­nu­cleo­ti­de pro­bes. Sys­tem. Appl. Mi­cro­bi­ol. 27:565-572 (2004).  PubMed
Brinkmeyer, R., F.-O. Glöckner, E. Helmke, and R. Amann: Pre­do­mi­nan­ce of Î²-pro­te­ob­ac­te­ria in sum­mer melt pools on Arc­tic pack ice. Lim­nol. Ocea­no­gr. 49(4):1013-1021 (2004).  ASLO  Full Text
Dubilier, N.: Mul­ti­ple bac­te­ri­al en­do­sym­bi­onts in gut­less ma­ri­ne worms: com­pe­ti­tors or part­ners? Nova Acta Leo­pol­di­na N.F. 88:107-112 (2004).
Gillan, D.C. and N. Dubilier.: No­vel epi­bio­tic Thiothrix bac­te­ri­um on a ma­ri­ne am­phi­pod. Appl. En­vi­ron. Mi­cro­bi­ol. 70(6):3772-3775 (2004).  PubMed  Full Text
Ishii, K., M. Mußmann, B. J. MacGregor, and R. Amann: An im­pro­ved fluo­re­scence in situ hy­bri­di­za­t­i­on pro­to­col for the iden­ti­fi­ca­ti­on of bac­te­ria and ar­chaea in ma­ri­ne se­di­ments. FEMS Mi­cro­bi­ol. Ecol. 50:203-212 (2004).  PubMed
Oren, A., F. Rodriguez-Valera, J. Anton, S. Benlloch, R. Rosselló-Mora, R. Amann, J. Coleman, and N. J. Russell: Chap­ter 3. Red, ex­tre­me­ly ha­lo­phi­lic, but not ar­chae­al: the phy­sio­lo­gy and eco­lo­gy of Salinibacter ruber, a bac­te­ri­um iso­la­ted from sal­tern crys­tal­li­zer ponds. pp. 63-76, In: Ha­lo­phi­lic mi­cro­or­ga­nisms, A. Ven­to­sa. (ed.). Sprin­ger-Ver­lag, Ber­lin Hei­del­berg (2004).  Springer
Peplies, J., S. C. K. Lau, J. Pernthaler, R. Amann, and F. O. Glöckner: Ap­p­li­ca­ti­on and va­li­da­ti­on of DNA mi­cro­ar­rays for the 16S rRNA-ba­sed ana­ly­sis of ma­ri­ne bac­te­rio­plank­ton. En­vi­ron. Mi­cro­bi­ol. 6(6):638-645 (2004).  PubMed
Pernthaler, A. and R. Amann: Si­mul­ta­neous fluo­re­scence in situ hy­bri­di­za­t­i­on of mRNA and rRNA in en­vi­ron­men­tal bac­te­ria. Appl. En­vi­ron. Mi­cro­bi­ol. 70(9):5426-5433 (2004).  PubMed  Full Text
Pernthaler, A., J. Pernthaler, and R. Amann: Sen­si­ti­ve mul­ti-co­lor fluo­re­scence in situ hy­bri­di­za­t­i­on for the iden­ti­fi­ca­ti­on of en­vi­ron­men­tal mi­cro­or­ga­nisms. In: Mole­cu­lar Mi­cro­bi­al Eco­lo­gy Ma­nu­al, Se­cond Edi­ti­on, 3.11. pp. 711-726, Ko­wal­chuk, G. et al. (Eds.), Klu­wer Aca­de­mic Pu­blis­hers, Dor­drecht, The Nether­lands (2004).  Springer
Pernthaler, J., E. Zöllner, F. Warnecke, and K. Jürgens: Bloom of fil­amen­tous bac­te­ria in a me­so­tro­phic lake: Iden­ti­ty and po­ten­ti­al con­trol­ling me­cha­nism. Appl. En­vi­ron. Mi­cro­bi­ol. 70(10):6272-6281 (2004).  PubMed  Full Text
Sekar, R., B. M. Fuchs, R. Amann, and J. Pernthaler: Flow sor­ting of ma­ri­ne bac­te­rio­plank­ton af­ter fluo­re­scence in situ hy­bri­di­za­t­i­on. Appl. En­vi­ron. Mi­cro­bi­ol. 70(10):6210-6219 (2004).  PubMed  Full Text
Teira, E., T. Reinthaler, A. Pernthaler, J. Pernthaler, and G. J. Herndl: Com­bi­ning ca­ta­ly­zed re­por­ter de­po­si­ti­on-fluo­re­scence in situ hy­bri­di­za­t­i­on and mi­cro­au­to­ra­dio­gra­phy to de­tect sub­stra­te uti­liza­t­i­on by Bac­te­ria and Ar­chaea in the deep oce­an. Appl. & En­vi­ron. Mi­cro­bi­ol. 70(7):4411-4414 (2004).  PubMed  Full Text
Warnecke, F., R. Amann, and J. Pernthaler: Ac­tino­bac­te­ri­al 16S rRNA ge­nes from freshwa­ter ha­bi­tats clus­ter in four dis­tinct li­na­ges. En­vi­ron. Mi­cro­bi­ol. 6(3):242-253 (2004).  PubMed
Zubkov M., L. J. Linn, R. Amann, and R. P. Kiene: Tem­po­ral pat­terns of bio­lo­gi­cal di­me­thyl­sul­fi­de (DMS) con­sump­ti­on du­ring la­bo­ra­to­ry-in­du­ced phy­to­plank­ton bloom cy­cles. Mar. Ecol. Prog. Ser. 271:77-86 (2004).  NERC
Zubkov, M. V., G. A. Tarran, and B. M. Fuchs: Depth re­la­ted ami­no acid uptake by Prochlorococcus cya­no­bac­te­ria in the Sou­thern At­lan­tic tro­pi­cal gyre. FEMS Mi­cro­bi­ol. Ecol. 50:153-161 (2004).  PubMed
Ph.D. thesis
Warnecke, Falk: Di­ver­si­tät und Öko­lo­gie von lim­ni­schen Ac­tino­bak­te­ri­en. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men  (2004), 139pp.

Flux Group

Boetius, A., Suess, E.: Hy­dra­te Ridge: A na­tu­ral la­bo­ra­to­ry for the stu­dy of mi­cro­bi­al life fu­e­led by me­tha­ne from near-sur­face gas hy­dra­tes. Che­mi­cal Geo­lo­gy 205:291-310 (2004).  ScienceDirect
Ehrenhauss, S., Witte, U., Janssen, F., Huettel, M.: De­com­po­si­ti­on of dia­toms and nut­ri­ent dy­na­mics in per­me­able North Sea se­di­ments. Con­ti­nen­tal Shelf Re­se­arch 24:721-737 (2004).  ScienceDirect
Ehrenhauss, S., Witte, U., Bühring, S., Hüttel, M.: Ef­fect of ad­vec­tive pore wa­ter trans­port on dis­tri­bu­ti­on and de­gra­da­ti­on of dia­toms in per­me­able North Sea se­di­ments. Ma­ri­ne Eco­lo­gy Pro­gress Se­ries 271:99-111 (2004).  MEPS
Ehrenhauss, S. and Huettel, M.: Ad­vec­tive trans­port and de­com­po­si­ti­on of chain-for­ming plank­to­nic dia­toms in per­me­able se­di­ments. Jour­nal of Sea Re­se­arch 52:179-197 (2004).  ScienceDirect
Hensen, C., Pfeifer K., Wenzhöfer F., Volbers A., Schulz S., Holstein J., Romero O., Seiter K.: Flu­xes at the bent­hic boun­da­ry lay­er - A glo­bal view from the South At­lan­tic. pp. 401-430, In: The South At­lan­tic in the late Qua­tern­ary. G. We­fer, S. Mu­litza, V. Rat­mey­er (eds.), Sprin­ger Vlg. Ber­lin (2004).
Joye, S. B., Boetius, A., Orcutt, B.N., Montoya, J. P., Schulz, H. N., Erickson, M. J., Lugo, S. K.: The an­ae­ro­bic oxi­da­ti­on of me­tha­ne and sul­fa­te re­duc­tion in se­di­ments from Gulf of Me­xi­co cold seeps. Che­mi­cal Geo­lo­gy 205:219-238 (2004).  ScienceDirect
Orcutt, B.N., Boetius, A., Lugo, S. K., MacDonald, I. R., Samarkin, V. A., Joye, S. B.: Life at the edge of me­tha­ne ice: mi­cro­bi­al cy­cling of car­bon and sul­fur in Golf of Me­xi­co gas hy­dra­tes. Che­mi­cal Geo­lo­gy 205:239-251 (2004).  ScienceDirect
Precht, E. and M. Huettel: Ra­pid wave-dri­ven ad­vec­tive pore wa­ter ex­ch­an­ge in a per­me­able co­as­tal se­di­ment. Jour­nal of Sea Re­se­arch 51:93-107.  ScienceDirect
Precht, E., U. Franke, L. Polerecky, and M. Huettel: Oxy­gen dy­na­mics in per­me­able se­di­ments with wave-dri­ven pore wa­ter ex­ch­an­ge. Lim­nol. Ocea­no­gr. 49(3):693-705.  ASLO  Full Text
Rasheed, M., Wild, C., Franke, U. and Huettel, M.: Bent­hic pho­to­syn­the­sis and oxy­gen con­sump­ti­on in per­me­able car­bo­na­te se­di­ments at He­ron Is­land, Gre­at Bar­ri­er Reef, Aus­tra­lia. Es­tua­ri­ne Co­as­tal and Shelf Sci­ence 59:139-150 (2004).  ScienceDirect
Reimers, C. E., Stecher, H. A., Taghon, G. L., Fuller, C. M., Huettel, M., Rusch, A., Ryckelynck, N. and Wild, C.: In situ mea­su­re­ments of ad­vec­tive so­lu­te trans­port in per­me­able shelf sands. Con­ti­nen­tal Shelf Re­se­arch 24:183-201 (2004).  Ingenta
Røy, H., Huettel, M., Jørgensen, B B.: Trans­mis­si­on of oxy­gen con­cen­tra­ti­on fluc­tua­ti­ons through the dif­fu­si­ve boun­da­ry lay­er over­ly­ing aqua­tic se­di­ments. Lim­no­lo­gy and Ocea­no­gra­phy 49(3):686-692 (2004).  RefDoc
Saidi, A. and Kim, J.: Heat Flux Sen­sor with Mi­ni­mal Im­pact on Boun­da­ry Con­di­ti­ons. Exp. Ther­mal and Flu­id Sci­ence 28:903-908 (2004).  ScienceDirect
Stöhr, M. Goharzadeh, A. and Khalili, A.: In­ves­ti­ga­ti­on of flow and trans­port in the vicini­ty of upri­sing bub­bles near the in­ter­face of per­me­able se­di­ments using 3D PLIF and PIV. pp. 1-11, In:  Pro­cee­ding of 12th In­ter­na­tio­nal­Sym­po­si­um on Ap­p­li­ca­ti­ons of La­ser Tech­ni­ques to Flu­id Me­cha­nics, Lis­bon (2004).  ResearchGate  Full Text
Wild, C., Tollrian, R. and Huettel, M.: Ra­pid re­cy­cling of co­ral mass spaw­ning pro­ducts in per­me­able reef se­di­ments. Ma­ri­ne Eco­lo­gy Pro­gress Se­ries 271:159-166 (2004).
Wild, C., M. Huettel, A. Klueter, S. G. Kremb, M.Y.M. Rasheed and B. B. Jørgensen:  Co­ral  mu­cus func­tions as en­er­gy car­ri­er and par­ti­cle trap in the reef eco­sys­tem. Na­tu­re 428:66-70  (2004).  PubMed
Wild, C., Rasheed, M., Werner, U., Franke, U., Johnstone, R. and Huettel, M.: De­gra­da­ti­on and mi­ne­ra­liza­t­i­on of co­ral mu­cus in reef en­vi­ron­ments. Ma­ri­ne Eco­lo­gy Pro­gress Se­ries 267, 159-171 (2004).  MEPS
Ph.D. theses
Bühring, Solveig: Mi­cro­bi­al car­bon pro­ces­sing in ma­ri­ne se­di­ments: Case stu­dies in North Sea sands and oli­go­tro­phic deep-sea se­di­ments.Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 185pp.
Janssen, Felix: Pore-wa­ter ad­vec­tion and or­ga­nic mat­ter mi­ne­ra­liza­t­i­on in North Sea shelf sands. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 189pp.
Treude, Tina: An­ae­ro­bic oxi­da­ti­on of me­tha­ne in ma­ri­ne se­di­ments. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 272pp.

Mi­cro­bi­al Ge­no­mics Group

Bauer, M., Lombardot, T., Teeling, H., Naomi, W., Amann, R.I., Glöckner, F.O.: Ar­chaea-like Ge­nes for C1-Trans­fer En­zy­mes in Planctomycetes: Phy­lo­ge­ne­tic Im­pli­ca­ti­ons of Their Un­ex­pec­ted Pre­sence in This Phyl­um. Jour­nal of Mole­cu­lar Evo­lu­ti­on 59:571-586 (2004).  PubMed
Glöckner, F. O.: Um­welt­ge­no­mik mit Pirellula. Bio­spek­trum 3:262-263 (2004). Full Text
Heuchert, A., F. O. Glöckner, R. Amann, and U. Fischer: Psychrobacter nivimaris sp. nov.*, a he­te­ro­tro­phic bac­te­ri­um at­ta­ched to or­ga­nic par­ti­cles iso­la­ted from the South At­lan­tic (Ant­arc­tica). Syst. Appl. Mi­cro­bi­ol. 27:399-406 (2004).  PubMed
Peplies, J., F. O. Glöckner, R. Amann, and W. Ludwig: Com­pa­ra­ti­ve se­quence ana­ly­sis and oli­go­nu­cleo­ti­de pro­be de­sign ba­sed on the 23S rRNA ge­nes of Alphaproteobacteria from North Sea bac­te­rio­plank­ton. Sys­tem. Appl. Mi­cro­bi­ol. 27:573-580 (2004).  PubMed
Teeling, H., T. Lombardot, M. Bauer, W. Ludwig, and F. O. Glöckner: Eva­lua­ti­on of the phy­lo­ge­ne­tic po­si­ti­on of the planc­to­my­ce­te "Rhodopirellula baltica SH 1" by me­ans of con­ca­te­n­a­ted ri­bo­so­mal pro­te­in se­quen­ces, DNA-di­rec­ted RNA po­ly­me­ra­se sub­u­nit se­quen­ces and who­le ge­no­me trees. Int. J. Syst. Evol. Mi­cro­bi­ol. 54:791-801 (2004).  PubMed  Full Text
Teeling, H., A. Meyerdierks, M. Bauer, R. Amann, and F. O. Glöckner: Ap­p­li­ca­ti­on of Te­tra­nu­cleo­ti­de Fre­quen­cies for the As­si­gn­ment of Ge­no­mic Frag­ments. En­vi­ron. Mi­cro­bi­ol. 6(9):938-947 (2004).  PubMed
Teeling, H., J. Waldmann, T. Lombardot, M. Bauer, and F. O. Glöckner: TE­TRA: a web-ser­vice and a stand-alo­ne pro­gram for the ana­ly­sis and com­pa­ri­son of te­tra­nu­cleo­ti­de usa­ge pat­terns in DNA se­quen­ces. BMC Bio­in­for­ma­tics 5:163 (2004).  PubMed  Full Text
Diploma theses
Richter, Michael: Bio­in­for­ma­ti­scher Ge­nom­ver­gleich der sul­fat­re­du­zie­ren­den Bak­te­ri­en Desulfotalea psychrophila und Desulfovibrio vulgaris (2004).
Wecker, Patricia: Ver­su­che zur Ent­wick­lung ei­nes ge­ne­ti­schen Sys­tems für Rhodopirellula baltica SH1T (2004).
Ph.D. theses
Lombardot, Thierry: The ge­no­me of the free-li­ving, ma­ri­ne Planctomycete Pirellula sp. strain 1 ("Rhodopirellula baltica"): Bio­in­for­ma­tics and Bio­lo­gy. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 155pp.
Teeling, Hanno: As­pek­te der bio­in­for­ma­ti­schen Ana­ly­se und An­no­ta­ti­on des Ge­noms von Rhodopirellula baltica T. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 136pp.

Mi­cro­sen­sor Group

Altmann, D., Stief, P., Amann, R., De Beer,D.: Ni­tri­fi­ca­ti­on in freshwa­ter se­di­ments as in­flu­en­ced by in­sect lar­vae: Quan­ti­fi­ca­ti­on by mi­cro­sen­sors and fluo­re­scence in situ hy­bri­di­za­t­i­on. Mi­cro­bi­al Eco­lo­gy 48:145-153 (2004).  PubMed
Altmann, D., Stief, P., Amann, R., de Beer, D.: Dis­tri­bu­ti­on and ac­tivi­ty of ni­tri­fy­ing bac­te­ria in na­tu­ral stream se­di­ment ver­sus la­bo­ra­to­ry se­di­ment mi­cro­cosms. Aqua­tic Mi­cro­bi­al Eco­lo­gy 36(1):73-81 (2004). Full Text
De Beer, D.,  Wenzhöfer, F., Ferdelman, T.G., Boehme, S., Huettel, M., van Beusekom, J.E.E., Boettcher, M.E., Musat, N., Dubilier, N.: Trans­port and mi­ne­ra­liza­t­i­on ra­tes in North Sea san­dy in­terti­dal se­di­ments (Sylt-Rømø Ba­sin, Wad­den Sea). Lim­no­lo­gy and Ocea­no­gra­phy 50(1):113-127 (2005).  ePIC
Garcia-Pichel, F., Al-Horani, F.A., Farmer, J.D., Ludwig, R., Wade, B.D.: Ba­lan­ce bet­ween mi­cro­bi­al cal­ci­fi­ca­ti­on and me­ta­zo­an bio­ero­si­on in mo­dern stroma­to­li­tic on­co­li­tes. Geo­bio­lo­gy 2:49-57 (2004).  Wiley
Gieseke, A. and De Beer, D.:Use of mi­cro­elec­tro­des to mea­su­re in situ mi­cro­bi­al ac­tivi­ties in bio­films, se­di­ments, and mi­cro­bi­al mats. In: Mole­cu­lar Mi­cro­bi­al Eco­lo­gy Ma­nu­al (2nd edi­ti­on). Ko­wal­chuk G.G., de Brui­jn F.J., Head I.M., Ak­ker­m­ans A.D., van El­sas J.D. (eds.), Hei­del­berg. Sprin­ger (2004), 30pp.  Springer
Grötzschel, S., Koester, J., De Beer, D.: De­gra­da­ti­on of 2,4-di­chlo­ro­phen­ox­ya­ce­tic acid (2,4-D) by a hy­per­sa­li­ne mi­cro­bi­al mat and re­la­ted func­tio­nal chan­ges in the mat com­mu­ni­ty. Mi­cro­bi­al Eco­lo­gy 48:254-262 (2004).  PubMed
Grunwald, B., G. Holst: Fib­re op­tic re­frac­tive in­dex mi­cro­sen­sor ba­sed on whi­te-light SPR ex­ci­ta­ti­on. Sen­sors and Ac­tua­tors A 113:174-180 (2004).  ScienceDirect
Grunwald, B. and Kühl, M.: A sys­tem for ima­ging va­ria­ble chlo­ro­phyll fluo­re­scence of aqua­tic pho­to­tro­phs. Ophe­lia 58(2):79-89 (2004).  TFO
Henning, D., G.-P. Zauke, P. Stief and E. Vareschi: In­te­gra­ted ef­fects of ma­ri­ne bent­hic pho­to­syn­the­ti­cal­ly ac­tive mi­cro­or­ga­nisms and a bio­tur­ba­ting po­ly­chae­te, Hediste diversicolor (O.W. Mül­ler), on oxy­gen dis­tri­bu­ti­on at the se­di­ment-wa­ter in­ter­face: A geo­sta­tis­ti­cal ana­ly­sis. pp. 271-287. In T. Ni­shi­da et al. (eds.), Proc. 2nd Int. Symp. GIS, Vol. 2, Fis­he­ry Aqua­tic re­serach Group, Ka­wa­goe-City, Ja­pan (2004).  ResearchGate  Full Text
Kiørboe, T., Grossart, H.-P., Ploug, H., Tang, K., Auer, B.: Par­ti­cle-as­so­cia­ted fla­gel­la­tes: swim­ming pat­terns, co­lo­niza­t­i­on ra­tes, and gra­zing on at­ta­ched bac­te­ria. Aqua­tic Mi­cro­bi­al Eco­lo­gy 35:141-152 (2004).  AME
Smith, S. M., Abed, R. M. M., Garcia-Pichel, F.: Bio­lo­gi­cal soil crusts of sand du­nes in Cape Cod Na­tio­nal Seas­hore, Mas­sa­chu­setts, USA. Mi­cro­bi­al Eco­lo­gy 48:200-208 (2004).  PubMed
Stehning, C. and G.A. Holst: Ad­dres­sing Mul­ti­ple In­di­ca­tors on a Sin­gle Op­ti­cal Fi­ber - Di­gi­tal Si­gnal Pro­ces­sing Ap­proa­ches for Tem­pe­ra­tu­re Com­pen­sa­ted Oxy­gen Sen­sing. IEEE Sen­sors Jour­nal 4(1):153-159 (2004).  IEEexplore
Stief, P., Altmann, D., de Beer, D., Bieg, R., Kureck, A.: Mi­cro­bi­al ac­tivi­ties in the bur­row en­vi­ron­ment of the po­ta­mal may­fly Ephoron virgo. Freshwa­ter Bio­lo­gy 49:1152-1163 (2004).  Wiley
Tarre, S., Beliavski, M., Denekamp, N., Gieseke, A., de Beer, D., Green, M.: High ni­tri­fi­ca­ti­on rate at low pH in a flui­di­zed bed re­ac­tor with chalk as the bio­film car­ri­er. Wa­ter Sci­ence Tech­no­lo­gy 49(11):95-105 (2004).  PubMed
Diploma theses
Schoon, Raphaela: Com­pa­ri­son of Dif­fe­rent Tech­ni­ques for Mea­su­ring Pho­to­syn­the­sis in Fo­ra­mi­ni­fe­ra (2004).
Ph. D. theses
Ludwig, Rebecca: Car­bon cy­cling and cal­ci­fi­ca­ti­on in hy­per­sa­li­ne mi­cro­bi­al mats. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2004), 163pp.
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