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Pu­bli­ka­tio­nen 2008

Pu­bli­ka­tio­nen 2008

De­part­ment of Bio­geo­che­mis­try

Arning, E. T., D. Birgel, H. N. Schulz-Vogt, L. Holmkvist, B. B. Jørgensen, A. Larson and J. Peckmann:  Li­pid bio­mar­ker pat­terns of phos­pho­ge­nic se­di­ments for up­wel­ling re­gi­ons. Geo­mi­cro­bio­lo­gy Jour­nal 25(2):69-82 (2008).  TFO
Boudreau, B. P., C. Arnosti, B. B. Jørgensen and D. E. Canfield:  Com­ment on "Phy­si­cal Mo­del for the De­cay and Pre­ser­va­ti­on of Ma­ri­ne Or­ga­nic Car­bon". Sci­ence 319:1616b (2008).  PubMed  Full Text
Dale, A. W., D. R. Aguilera, P. Regnier, H. Fossing, N. J. Knab and B. B. Jørgensen:  Sea­so­nal dy­na­mics of the depth and rate of an­ae­ro­bic oxi­da­ti­on of me­tha­ne in Aar­hus Bay (Den­mark) se­di­ments. Jour­nal of Ma­ri­ne Re­se­arch 66:127-155 (2008).  IC
Dale, A. W., P. Regnier, N. J. Knab, B. B. Jørgensen and P. Van Cappellen:  An­ae­ro­bic oxi­da­ti­on of me­tha­ne (AOM) in ma­ri­ne se­di­ments from the Ska­ger­rak (Den­mark): II. Re­ac­tion-trans­port mo­de­ling. Geochi­mi­ca et Cos­mochi­mi­ca Acta 72:880–2894 (2008).  ScienceDirect
Finke, N. and B. B. Jørgensen:  Re­s­pon­se of fer­men­ta­ti­on and sul­fa­te re­duc­tion to ex­pe­ri­men­tal tem­pe­ra­tu­re chan­ges in tem­pe­ra­te and Arc­tic ma­ri­ne se­di­ments. The ISME Jour­nal 2: 815-829 (2008).  PubMed  Full Text
Furrer H., Schaltegger U., Ovtcharova M. and P. Meister: U-Pb zir­con age of vol­ca­ni­clas­tic lay­ers in Midd­le Tri­as­sic plat­form car­bo­na­tes of the Aus­tro­al­pi­ne Sil­vret­ta nap­pe (Swit­z­er­land). Swiss J. Geo­sci. 101:595–603 (2008).  Springer  Full Text
Khalili, A., K. Javadi, A. Saidi, A. Goharzadeh, M. Huettel and B. B. Jørgensen:  On ge­ne­ra­ting uni­form bot­tom she­ar stress. Part I: A quan­ti­ta­ti­ve stu­dy of mi­cro­cosm cham­bers. Re­cent Pa­tents on Che­mi­cal En­gi­nee­ring 1:174-191 (2008).  BenthamScience  Full Text
Knab, N. J., A. W. Dale, K. Lettmann, H. Fossing and B. B. Jørgensen:  Ther­mo­dy­na­mic and ki­ne­tic con­trol on an­ae­ro­bic oxi­da­ti­on of me­tha­ne in ma­ri­ne se­di­ments. Geochi­mi­ca et Cos­mochi­mi­ca Acta 72:3746-3757 (2008).  ScienceDirect
Knab, N. J., B. A. Cragg, C. Borowski, R. J. Parkes, R. Pancost and B. B. Jørgensen:  An­ae­ro­bic oxi­da­ti­on of me­tha­ne (AOM) in ma­ri­ne se­di­ments from the Ska­ger­rak (Den­mark): I. Geo­che­mi­cal and mi­cro­bio­lo­gi­cal ana­ly­ses. Geochi­mi­ca et Cos­mochi­mi­ca Acta 72:2868–2879 (2008).  ScienceDirect
Knab, N. J., B. A. Cragg, E.R.C. Hornibrook, L. Holmkvist, C. Borowski, R. J. Parkes and B. B. Jørgensen:  Re­gu­la­ti­on of an­ae­ro­bic me­tha­ne oxi­da­ti­on in se­di­ments of the Black Sea. Bio­geo­sci­en­ces Dis­cuss. 5:2305-2341 (2008).  ORCA  Full Text
Meister, P., Bernasconi, S.M., Vasconcelos, C. and McKenzie, J.A.:  Sea­le­vel chan­ges con­trol dia­ge­ne­tic do­lo­mi­te for­ma­ti­on in he­mi­pel­agic se­di­ments of the Peru Mar­gin. Ma­ri­ne Geo­lo­gy 252(3-4):166-173 (2008).  ScienceDirect
Musat, N., H. Halm, B. Winterholler, P. Hoppe, S. Peduzzi, F. Hillion, F. Horreard, R. Amann, B. B. Jørgensen and M. M. M. Kuypers: A sin­gle-cell view on the eco­phy­sio­lo­gy of an­ae­ro­bic pho­to­tro­phic bac­te­ria. PNAS 105(46):17861-17866 (2008).  PubMed  Full Text
Nickel, M., V. Vandieken, V. Brüchert and B. B. Jørgensen: Mi­cro­bi­al Mn(IV) and Fe(III) re­duc­tion in nort­hern Ba­rents Sea se­di­ments un­der dif­fe­rent con­di­ti­ons of ice co­ver and or­ga­nic car­bon de­po­si­ti­on. Deep-Sea Re­se­arch II 55:2390-2398 (2008).  USD
Neubert N., Nägler T.F. and Böttcher M.E.: Sul­fi­di­ty con­trols mo­lyb­de­num iso­to­pe dis­cri­mi­na­ti­on into eu­xi­nic se­di­ments: Evi­dence from the mo­dern Black Sea. Geo­lo­gy 36:775-778 (2008).  Geology
Schwermer, C.U., Lavik, G., Abed, R.M.M., Dunsmore, B., Ferdelman, T.G., Stoodley, P., Gieseke, A., de Beer, D.: Sea-le­vel chan­ges con­trol of bac­te­ri­al bio­film com­mu­nities in pipe­lines used for in­jec­tion of sea­wa­ter into oil fiel­ds. Appl.and En­vi­ron. Mi­cro­bi­ol. 74:2841-285 (2008).
Wild, C., Mayr, C., Wehrmann, L., Schöttner, S.I., Naumann, M., Hoffmann, F. and Rapp, H.T.: Or­ga­nic mat­ter re­lease by cold wa­ter co­rals and its im­pli­ca­ti­on for fau­na–mi­cro­be in­ter­ac­tion. Ma­ri­ne Eco­lo­gy Pro­gress Se­ries 372:67-75 (2008).  MEPS
B.Sc theses
Landwehrkamp, Lukas:  De­ter­mi­na­ti­on of in situ me­tha­ne con­cen­tra­ti­ons in ma­ri­ne se­di­ments by ana­ly­sis of void gas with gas chro­ma­to­gra­phy. Uni­ver­si­ty of Es­sen (2008).
M.Sc theses
Voßmeyer, Antje:  Ef­fects of Pres­su­re on Deep Sea An­ae­ro­bic Bio­geo­che­mi­cal Pro­ces­ses.  (2008).
Ph.D. theses
Julies, Elsabé M.: Mi­cro­bi­al eco­lo­gy of an­ae­ro­bic car­bon mi­ne­ra­liza­t­i­on in Na­mi­bi­an shelf se­di­ments. PhD the­sis, Mar­Mic, Uni­ver­si­tät Bre­men, Bre­men (2008), 183pp.
Schläppy, Marie-Lise:Che­mi­cal mi­cro-en­vi­ron­ments, ven­ti­la­ti­on be­ha­vi­or and mi­cro­bi­al pro­ces­ses in spon­ges. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2008), 155pp.

Mi­cro­sen­sor Group

Abed, R. M. M., Kohls K., Schoon R., Scherf A. K., Schacht M., Palinska K. A., Al-Hassani H., Hamza W., Rullkotter J., Golubic S.:  Li­pid bio­mar­kers, pig­ments and cya­no­bac­te­ri­al di­ver­si­ty of mi­cro­bi­al mats across in­terti­dal flats of the arid co­ast of the Ara­bi­an Gulf (Abu Dha­bi, UAE). FEMS Mi­cro­bio­lo­gy Eco­lo­gy 65(3):449-462 (2008).  PubMed
Bachar, A., Polerecky L., Fisher J., Vamvakopoulos K., de Beer D., Jonkers H.M.:  Two-di­men­sio­nal map­ping of pho­to­pig­ment dis­tri­bu­ti­on and ac­tivi­ty of Chloroflexus-like bac­te­ria in a hy­per­sa­li­ne mi­cro­bi­al mat. FEMS Mi­crob. Ecol. 65:434-448 (2008).  PubMed
Beutler, M., Makrogianneli K., Vermeij R.J., Keppler M., Ng T., Jovin T.M. and Heintzmann R.: sat­FRET: esti­ma­ti­on of Förs­ter re­so­nan­ce en­er­gy trans­fer by ac­cep­tor sa­tu­ra­ti­on. Eur. Bio­phys. J. 38(1):69-82 (2008).  PubMed  Full Text
Bissett, A., de Beer D., Schoon R., Shiraishi F., Reimer A., Arp G.:  Mi­cro­bi­al me­dia­ti­on of stroma­to­li­te for­ma­ti­on in karst-wa­ter creeks. Lim­nol. Ocea­no­gr. 53(3):1159-1168 (2008).  ASLO  Full Text
Bissett, A., Reimer A., de Beer D., Shiraish, F., Arp G.: Me­ta­bo­lic mi­cro­en­vi­ron­men­tal con­trol by pho­to­syn­the­tic bio­films un­der chan­ging ma­cro­en­vi­ron­men­tal tem­pe­ra­tu­re and pH con­di­ti­ons. Appl. En­vi­ronm. Mi­cro­bi­ol. 74(20):6306-6312 (2008).  PubMed  Full Text
Bissett, A., Bowman, J.P., Burke, C.M.: Flav­o­bac­te­ri­al re­s­pon­se to or­ga­nic pol­lu­ti­on. Aqua­tic Mi­cro­bi­al Eco­lo­gy 51(1):31-43 (2008).  PubMed  Full Text
de Beer, D., Bissett A., de Wit R., Jonkers H., Köhler-Rink S., Nam H., Kim B.H., Eickert G., and Grinstain M.: A mi­cro­sen­sor for car­bo­na­te ions sui­ta­ble for mi­cro­pro­filing in freshwa­ter and sa­li­ne en­vi­ron­ments. Lim­nol Ocea­no­gr Me­thods 6:532-541 (2008).  ASLO  Full Text
De Deckker, P., Abed R. M. M., de Beer D., Hinrichs K.-U., O'Loingsigh T., Schefuß E., Stuu, J. W., Tapper N.J., van der Kaars S.: Geo­che­mi­cal and mi­cro­bio­lo­gi­cal fin­ger­prin­ting of air­bor­ne dust that fell in Can­ber­ra, Aus­tra­lia, in Oc­to­ber 2002. Geo­chem. Geo­phys. Geo­syst. 9(12):doi:10.1029/​2008G­C002091, 1-22 (2008).  Wiley  Full Text
Foesel, B. U., Gieseke A., Schwermer C., Stief P., Koch L., Cytryn E., de la Torré J. R., van Rijn J., Minz D., Drake H. L., Schramm A.:  Ni­tro­so­mo­nas Nm143-like am­mo­nia oxi­di­zers and Nitrospira marina-like ni­tri­te oxi­di­zers do­mi­na­te the ni­tri­fier com­mu­ni­ty in a ma­ri­ne aqua­cul­tu­re bio­film. FEMS Mi­cro­bio­lo­gy Eco­lo­gy 63(2):192-204 (2008).  PubMed
Grossart, H.-P., Jezbera J., K. Hornák, K.M.L. Hutalle, U. Buck and K Šimek: Top-down and bot­tom-up in­du­ced shifts in bac­te­ri­al ab­un­dance, pro­duc­tion and com­mu­ni­ty com­po­si­ti­on in an ex­pe­ri­men­tal­ly di­vi­ded hu­mic lake. En­vi­ron­men­tal Mi­cro­bio­lo­gy 10(3):635-652 (2008).  PubMed
Hoffmann, F., Røy H., Bayer K., Hentschel U., Pfannkuchen M., Brümmer F., de Beer D.: Oxy­gen dy­na­mics and trans­port in the Me­di­ter­ra­ne­an spon­ge Aplysina aerophoba. Mar. Biol. 153:1257-1264 (2008).  PubMed  Full Text
Hoffmann F., Schläppy M.-L.:  Spon­ges (Po­rife­ra) and spon­ge mi­cro­bes. In: En­cy­clo­pe­dia of Geo­bio­lo­gy, Hei­del­berg, Sprin­ger Ver­lag (2008).
Humphrey, C., Weber M., Lott C., Cooper T., Fabricius K.:  Ef­fects of  sus­pen­ded se­di­ments, dis­sol­ved in­or­ga­nic nut­ri­ents and sal­in­i­ty on fer­ti­li­sa­ti­on and em­bryo de­ve­lop­ment in the co­ral Acropora millepora (Eh­ren­berg, 1834). Co­ral Reefs 27(4):837-850 (2008).  Springer  Full Text
Jansen, S., Walpersdorf E., Werner U., Billerbeck M., Boettcher M., de Beer D.: Func­tio­n­ing of ti­d­al flats as in­fer­red from tem­po­ral and spa­ti­al dy­na­mics of O2, H2S an pH in their sur­face se­di­ments. Oce­an Dy­na­mics, doi 10.1007/​s10236-009-0179-4 (2008).  Springer  Full Text
Kühl, M., Polerecky L.:  Func­tio­nal and struc­tu­ral ima­ging of pho­to­tro­phic mi­cro­bi­al com­mu­nities and sym­bio­ses. Aqua­tic Mi­cro­bi­al Eco­lo­gy 53:99-118 (2008).  PubMed  Full Text
Martí­nez-Garcí­a, M., Stief P., Dí­az-Valdés M., Wanner G., Ramos-Esplá A., Dubilier N., Antón J.:  Am­mo­nia-oxi­di­zing Crenarchaeota and ni­tri­fi­ca­ti­on in­si­de the tis­sue of a co­lo­ni­al asci­di­an. En­vi­ron­men­tal Mi­cro­bio­lo­gy 10(11):2991-3001 (2008).  PubMed  Full Text
Ploug, H., Iversen M.H., Koski M., Buitenhuis E.T.:  Pro­duc­tion, oxy­gen re­spi­ra­ti­on ra­tes, and sin­king ve­lo­ci­ty of cope­pod fe­cal pel­lets: di­rect mea­su­re­ments of bal­las­ting by opal and cal­ci­te. Lim­nol. Ocea­no­gr. 53(2):469-476 (2008).  ASLO  Full Text
Ploug, H.: Cya­no­bac­te­ri­al sur­face blooms for­med by Aphanizomenon sp. and Nodularia spumigena in the Bal­tic Sea: Small-sca­le flu­xes, pH, and oxy­gen mi­cro­en­vi­ron­ments.  Lim­nol Ocea­no­gr. 53:914-921 (2008).  ASLO  Full Text
Polerecky, L., Lott C., Weber M.: In situ mea­su­re­ment of gross pho­to­syn­the­sis using a mi­cro­sen­sor-ba­sed light-shade shift me­thod. Lim­no­lo­gy and Ocea­no­gra­phy-Me­thods 6:373-383 (2008).  Full Text
Polerecky, L., Bissett A., Al-Najjar M., Faerber P., Osmers H., Suci P. A., Stoodley P., de Beer D.:  Mo­du­lar spec­tral ima­ging sys­tem for dis­cri­mi­na­ti­on of pig­ments in cells and mi­cro­bi­al com­mu­nities. Appl. En­vi­ronm. Mi­cro­bi­ol. 75(3):758-771 (2008).  PubMed  Full Text
Schreiber, F., Polerecky L., de Beer D.:  Nitric oxi­de mi­cro­sen­sor for high spa­ti­al re­so­lu­ti­on mea­su­re­ments in bio­films and se­di­ments. Anal. Chem. 80(4):1152-1158 (2008).  PubMed
Schwermer, C.U., Lavik G., Abed R. M. M., Dunsmore B., Ferdelman T.G., Stoodley P., Gieseke A., de Beer D.:  Im­pact of ni­tra­te on the struc­tu­re and func­tion of bac­te­ri­al bio­film com­mu­nities in pipe­lines used for in­jec­tion of sea­wa­ter into oil fiel­ds. Appl. En­vi­ronm. Mi­cro­bi­ol. 74(9):2841-2851 (2008).  PubMed  Full Text
Sher, Y., Schneider K., Schwermer C.U., van Rijn J.: Sul­fi­de-in­du­ced ni­tra­te re­duc­tion in the sludge of an an­ae­ro­bic di­ges­ter of a zero-di­sch­ar­ge re­cir­cu­la­ting ma­ri­cul­tu­re sys­tem. Wat. Res. 42(16):4386-4392 (2008).  PubMed
Shiraishi, F., A. Bissett, D. de Beer, A. Reimer and G. Arp: Pho­to­syn­the­sis, re­spi­ra­ti­on and exo­po­ly­mer Cal­ci­um-bin­ding in bio­film cal­ci­fi­ca­ti­on (West­er­hö­fer and De­inschwan­ger Creek, Ger­ma­ny). Geo­mi­cro­bio­lo­gy Jour­nal 25:83-94 (2008).  TFO
Shiraishi, F., Reimer A., Bisset A., de Beer D., and Arp G.:  Mi­cro­bi­al ef­fects on bio­film cal­ci­fi­ca­ti­on, am­bi­ent wa­ter che­mis­try and sta­ble iso­to­pe re­cor­ds in a high­ly su­per­sa­tu­ra­ted set­ting (West­er­hö­fer Bach, Ger­ma­ny). Pa­laeo­geo­gra­phy, Pa­laeo­cli­ma­to­lo­gy and Pa­laeo­e­co­lo­gy 262(1-2):91-106 (2008).  ScienceDirect
Stoodley, P., Wefel, J., Gieseke A., de Beer D., von Ohle C.:  Bio­film Plaque and Hydro­dy­na­mic Ef­fects on Mass Trans­fer, Fluo­ri­de De­li­very and Ca­ries. JADA 139(9):1182-1190 (2008).  PubMed
Werner, U., Blazejak A., Bird P., Eickert G., Schoon R., Abed R. M. M., Bissett A., de Beer D.: Mi­cro­bi­al pho­to­syn­the­sis in co­ral reef se­di­ments (He­ron Reef, Aus­tra­lia). Es­tua­ri­ne, Co­as­tal and Shelf Sci­ence 76(4):876-888 (2008).  ScienceDirect
Diploma, M.Sc and B.Sc theses
Ehrenberg, Julia: Ein­fluss von Stick­stoff­mon­oxid auf den Stick­stoff­kreis­lauf in Süß­was­ser­se­di­men­ten. Di­plom­ar­beit FH Wies­ba­den, Um­weltech­nik (2008).
Kopiniok, Celina:  De­ni­tri­fi­ca­ti­on In­du­ced Cal­ci­fi­ca­ti­on in Sa­li­ne Bio­films. (2008).
Nemeki, Stella:  Com­pa­ra­ti­ve Stu­dy of Bent­hic Re­spi­ra­ti­on in Si­li­ca­te and Car­bo­na­te Sands of the Is­lands Elba and Pia­no­sa (Tyr­rhe­ni­an Sea, Ita­ly). (2008).
Sivelgen, Duygu:  Com­pa­ra­ti­ve Stu­dy of Bent­hic Pri­ma­ry Pro­duc­tion in Si­li­ca­te and Car­bo­na­te Sands of the Is­lands Elba and Pia­no­sa (Tyr­rhe­ni­an Sea, Ita­ly). (2008).

Mi­cro­bi­al Ha­bi­tat Group

Allers, E., C. Niesner, C. Wild and J. Pernthaler:  Mi­cro­bes en­ri­ched in sea­wa­ter af­ter ad­di­ti­on of co­ral mu­cus. Appl. En­vi­ron. Mi­cro­bi­ol. 74(10):3274-3278 (2008).  PubMed  Full Text
Amaral-Zettler, L., J. Peplies, A. Ramette, B. Fuchs, W. Ludwig and F. O. Glöckner: Pro­cee­dings of the in­ter­na­tio­nal work­shop on Ri­bo­so­mal RNA tech­no­lo­gy, April 7–9, 2008, Bre­men, Ger­ma­ny. Syst. Appl. Mi­cro­bi­ol. 31:258-268 (2008).  PubMed
Bachar, A., L. Polerecky, J.P. Fischer, K. Vamvakopoulos, D. de Beer and H. Jonker: Two-di­men­sio­nal map­ping of pho­to­pig­ments dis­tri­bu­ti­on and ac­tivi­ty of Chlo­rof­le­xus-like bac­te­ria in a hy­per­sa­li­ne mi­cro­bi­al mat. FEMS Mi­cro­bio­lo­gy Eco­lo­gy 65:434-448 (2008).  PubMed
Bayer K., A. Siegl, S. Schmitt, F. Hoffmann and U. Hentschel:  Un­ra­vel­ling mi­cro­bi­al di­ver­si­ty and me­ta­bo­lism in ma­ri­ne spon­ges. Nova Acta Leo­pol­di­na 96:71-78 (2008).
Böer, S. I., C. Arnosti, J. E. E. van Beusekom and A. Boetius:  Tem­po­ral va­ria­ti­ons in mi­cro­bi­al ac­tivi­ties and car­bon tur­no­ver in sub­ti­dal san­dy se­di­ments. Bio­geo­sci­en­ces Dis­cus­sions 5:4271-4313 (2008).  Biogeosciences  Full Text
Boetius, A., T. Holler, K. Knittel, J. Felden and F.Wenzhöfer: The se­abed as na­tu­ral la­bo­ra­to­ry: Les­sons from un­cul­ti­va­ted me­tha­notro­phs. pp. 59-82, In: Un­cul­ti­va­ted Mi­cro­or­ga­nisms. Mi­cro­bio­lo­gy Mo­no­graphs,  S. Epstein (ed.), Sprin­ger Ver­lag (2008).  Springer
Dupré, S., G. Buffet, J. Mascle, J.-P. Foucher, S. Gauger, A. Boetius, C. Marfia, the AsterX Team, the Quest ROV Teamandthe BIONIL Scientific Party:  High-re­so­lu­ti­on map­ping of lar­ge gas emit­ting mud vol­ca­noes on the Egyp­ti­an con­ti­nen­tal mar­gin (Nile Deep Sea Fan) by AUV sur­veys. Ma­ri­ne Geo­phy­si­cal Re­se­ar­ches 29:275-290 (2008).  Springer  Full Text
Elvert, M. and H. Niemann:  Oc­cur­rence of unusu­al ste­ro­ids and ho­pano­ids de­ri­ved from ae­ro­bic me­tha­notro­phs at an ac­tive ma­ri­ne mud vol­ca­no. Org. Geo­chem. 39:167-177 (2008).  ScienceDirect
Engelen, B., K. Ziegelmüller, L. Wolf, B. Köpke, A. Gittel, H. Cypionka, T. Treude, S. Nakagawa, F. Inagaki, M. A. Lever and B. O. Steinsbu:  Fluids from the ocea­nic crust sup­port mi­cro­bi­al ac­tivi­ties wi­t­hin the deep bio­s­phe­re. Geo­mi­cro­bi­ol. J. 25:56-66 (2008).  TFO
Evrard, V., P. L. M. Cook, B. Veuger, M. Huettel, and J. J. Middelburg:  Tra­c­ing car­bon and ni­tro­gen in­cor­po­ra­ti­on and pa­thways in the mi­cro­bi­al com­mu­ni­ty of a pho­tic sub­ti­dal sand. Aquat. Mi­crob. Ecol. 53:257-269 (2008).  AME
Hoffmann, F., H. Røy, K. Bayer, U. Hentschel, M. Pfannkuchen, F. Brümmer, and D. de Beer:  Oxy­gen dy­na­mics and trans­port in the Me­di­ter­ra­ne­an spon­ge Aplysina aerophoba. Mar. Biol. 153:1257-1264 (2008).  PubMed  Full Text
Jacobs, J. L., A. C. Fasi, A. Ramette, J. J. Smith, R. Hammerschmidt and G. W. Sundin:  Iden­ti­fi­ca­ti­on and oni­on pa­tho­ge­ni­ci­ty of Burkholderia cepacia com­plex iso­la­tes from the oni­on rhi­zo­s­phe­re and oni­on field soil. Appl. En­vi­ron. Mi­cro­bi­ol. 74(10):3121-3129 (2008).  PubMed  Full Text
Kamp, A., H. Røy, and H. N. Schulz-Vogt:  Vi­deo-sup­por­ted ana­ly­sis of Beggiatoa fil­ament growth, bre­a­ka­ge, and mo­ve­ment. Mi­crob. Ecol. 56:484-491 (2008).  PubMed  Full Text
Kanzog, C., A. Ramette, N. V. Quéric, and M. Klages:  Re­s­pon­se of bent­hic mi­cro­bi­al com­mu­nities to chi­tin en­rich­ment: an in situ stu­dy in the deep Arc­tic Oce­an. Po­lar Biol. 32:105-112 (2008).  Springer  Full Text
Lösekann, T., A. Robador, H. Niemann, K. Knittel, A. Boetius, and N. Dubilier:  En­do­sym­bio­ses bet­ween bac­te­ria and deep-sea si­bog­li­nid tu­be­worms from an Arc­tic cold seep (Haa­kon Mos­by Mud Vol­ca­no, Ba­rents Sea). En­vi­ron. Mi­cro­bi­ol. 10(12):3237-3254  (2008).  PubMed
Niemann H. and M. Elvert:  Dia­gnostic li­pid bio­mar­ker and sta­ble car­bon iso­to­pe si­gna­tu­res of mi­cro­bi­al com­mu­nities me­dia­ting the an­ae­ro­bic oxi­da­ti­on of me­tha­ne with sulp­ha­te. Org. Geo­chem. 39:1668-1677 (2008).  ScienceDirect
Omoregie, E. O., V. Mastalerz, G. de Lange, K. L. Straub, A. Kappler, H. Røy, A. Stadnitskaia, J.-P. Foucher and A. Boetius:  Bio­geo­che­mis­try and com­mu­ni­ty com­po­si­ti­on of iron- and sul­fur-pre­ci­pi­ta­ting mi­cro­bi­al mats at the Chefren Mud Vol­ca­no (Nile Deep Sea Fan, Eas­tern Me­di­ter­ra­ne­an) Appl. En­vi­ron. Mi­cro­bi­ol. 74(10):3198-3215 (2008).  PubMed  Full Text
Rossel, P. E., J. S. Lipp, H. F. Fredricks, J. A.  Arnds, A. Boetius, M. Elvert and K.-U. Hinrichs:  In­tact po­lar li­pids of an­ae­ro­bic me­tha­notro­phic ar­chaea and as­so­cia­ted bac­te­ria. Org. Geo­chem. 39:992-999 (2008).  ScienceDirect
Røy H., J. S. Lee, S. Jansen and D. de Beer:  Tide-dri­ven deep po­re­wa­ter flow in in­terti­dal sand flats. Lim­nol. Ocea­no­gr. 53(4):1521-1530 (2008).  TNO  Full Text
Sweetman, A. K. and U. Witte:  Re­s­pon­se of an abys­sal ma­cro­fau­nal com­mu­ni­ty to a phy­to­de­tri­tal pul­se. Mar. Ecol. Prog. Ser. 355:73-84 (2008).  MEPS
Sweetman, A. K. and U. Witte:  Ma­cro­fau­nal re­s­pon­se to phy­to­de­t­ri­tus in a ba­thy­al Nor­we­gi­an fjord. Deep-Sea Res. I 55:1503-1514 (2008).  ScienceDirect
Wegener, G., H. Niemann, M. Elvert, K.-U. Hinrichs and A. Boetius:  As­si­mi­la­ti­on of me­tha­ne and in­or­ga­nic car­bon by mi­cro­bi­al com­mu­nities me­dia­ting the an­ae­ro­bic oxi­da­ti­on of me­tha­ne. En­vi­ron. Mi­cro­bi­ol. 10(9):2287-2298 (2008).  PubMed
Wegener, G., M. Shovitri, K. Knittel, H. Niemann, M. Hovland, and A. Boetius:  Bio­geo­che­mi­cal pro­ces­ses and mi­cro­bi­al di­ver­si­ty of the Gull­faks and Tom­me­li­ten me­tha­ne seeps (Nort­hern North Sea). Bio­geo­sci­en­ces. 5:1127–1144 (2008).  EBSCO  Full Text
Wild, C., C. Mayr, L. M. Wehrmann, S. Schöttner, M. Naumann, F. Hoffmann and H. T. Rapp: Or­ga­nic mat­ter re­lease by cold wa­ter co­rals and its im­pli­ca­ti­on for fau­na-mi­cro­be in­ter­ac­tion. Mar. Ecol. Prog. Ser. 372:67-75 (2008).  MEPS
Diploma, M.Sc and B.Sc theses
Girnth, Anne-Christin: Di­ver­si­ty of sul­fi­de-oxi­di­zing bac­te­ria at Amon Mud Vol­ca­no. Leib­niz Uni­ver­si­tät Han­no­ver (2008), 130pp.
Pfitzner, Barbara: Ver­glei­chen­de Un­ter­su­chun­gen der bak­te­ri­el­len Ge­mein­schaft in Riffsan­den ver­schie­de­ner Mi­ne­ral­struk­tur. LMU Mün­chen (2008).
Ufkes, Judith: Im­pact of in­crea­sed car­bon di­oxi­de con­cen­tra­ti­on on the struc­tu­re of mi­cro­bi­al com­mu­nities in ma­ri­ne se­di­ments. Di­plom­ar­beit Uni­ver­si­tät Bre­men, Bre­men (2008), 108pp.
Ph.D. theses
Böer, Simone: In­ves­ti­ga­ti­on of the dis­tri­bu­ti­on and ac­tivi­ty of bent­hic mi­cro­or­ga­nisms in co­as­tal ha­bi­tats. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2008), 217pp.
Wegener, Gunter: Me­tha­ne Oxi­da­ti­on and Car­bon As­si­mi­la­ti­on in Ma­ri­ne Se­di­ments. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2008), 153pp.

Ma­the­ma­ti­cal Mo­de­ling Group

Alam, M. and Khalili A.: In­sta­bi­li­ties and pat­terns in ho­ri­zon­tal­ly oscil­la­ting par­ti­cu­la­te sus­pen­si­on. Phy­si­cal Re­view E, doi: 10.1103/​Phys­Re­vE.77041305 (2008).  PubMed
Khalili, A.: Ma­the­ma­ti­cal mo­de­ling of dy­na­mic pro­ces­ses in ma­ri­ne sys­tems. Re­se­arch Re­port of Max Planck So­cie­ty  (2008).
Khalili, A., Javadi K., Said A., Goharzadeh A., Huettel M. and Jørgensen B.B.: On Ge­ne­ra­ting Uni­form Bot­tom She­ar Stress, Part I: A Quan­ti­ta­ti­ve Stu­dy of Mi­cro­cosm Cham­bers. Re­cent Pa­tents on Che­mi­cal En­gi­nee­ring 1(3):174-191 (2008).  BenthamScience  Full Text
Liu, B. and Khalili A.: Ac­ce­le­ra­ti­on of steady-sta­te lat­ti­ce Boltz­mann si­mu­la­ti­ons for ex­te­ri­or flows. Phy­si­cal Re­view E, doi: 10.1103/​Phys­Re­vE.78.056701 (2008).  PubMed
Matyka, M., Khalili A. and Koza Z.: Tor­tuo­si­ty-po­ro­si­ty re­la­ti­on in po­rous me­dia flow. Phy­si­cal Re­view E, doi: 10.1103/​Phys­Re­vE.78.026306 (2008).  PubMed
Morad, M.R. and Khalili A.: Tran­si­ti­on lay­er thick­ness in a flu­id-po­rous me­di­um of mul­ti-si­zed sphe­ri­cal beads. Ex­pe­ri­ments in Fluids 46(2):323-330 (2008).  Springer  Full Text

De­part­ment of Mi­cro­bio­lo­gy

Amann, R., W. Goebel, B. Reinhold-Hurek, B. Schink, and F. Widdel (eds.):  Life stra­te­gies of mi­cro­or­ga­nisms in the en­vi­ron­ment and in host or­ga­nisms. Nova Acta Leo­pol­di­na NF 96: 356 (2008).  Leopoldia
Faivre, D., N. Menguy, M. Pósfai and D. Schüler: En­vi­ron­men­tal pa­ra­me­ters af­fect the phy­si­cal pro­per­ties of fast-gro­wing ma­gne­to­so­mes. Ame­ri­can Mi­ne­ra­lo­gist 93:463-469 (2008).  HAL
Grundmann, O., Behrends A., Rabus R., Amann J., Halder T., Heider J., Widdel, F.:  Ge­nes en­co­ding the can­di­da­te en­zy­me for an­ae­ro­bic ac­tiva­ti­on of n-al­ka­nes in the de­ni­tri­fy­ing bac­te­ri­um, strain HxN1. En­vi­ron. Mi­cro­bi­ol. 10(2):376-385 (2008).  PubMed
Hünken, M., Harder J., Kirst G.O.:  Epi­phytic bac­te­ria on the Ant­arc­tic ice dia­tom Amphiprora kufferathii Man­gu­in clea­ve hy­dro­gen per­oxi­de pro­du­ced du­ring al­gal pho­to­syn­the­sis. Plant Biol. 10:519-526 (2008).  PubMed
Kamp, A., Røy H., Schulz-Vogt H.N.:  Vi­deo-sup­por­ted ana­ly­sis of Beggiatoa fil­ament growth, bre­a­ka­ge, and mo­ve­ment. Mi­crob. Ecol. 56:484-491 (2008).  PubMed  Full Text
Krüger, M., H. Wolters, M. Gehre, S.B. Joye and H.-H. Richnow: Tra­c­ing the slow growth of an­ae­ro­bic me­tha­ne-oxi­di­zing com­mu­nities by 15N-la­bel­ling tech­ni­ques. FEMS Mi­cro­bi­ol. Ecol. 63:401-411 (2008).  PubMed
Kühn, S.F. and Köhler-Rink S.: pH ef­fect on the sus­cep­ti­bi­li­ty to pa­ra­si­to­id in­fec­tion in the ma­ri­ne dia­tom Coscinodiscus spp. (Ba­cil­la­rio­phy­ceae). Mar. Biol. 154:109-116 (2008).  PubMed  Full Text
Liebner, S., J. Harder and D. Wagner:  Bac­te­ri­al di­ver­si­ty and com­mu­ni­ty struc­tu­re in po­ly­go­nal tun­dra soils from Sa­mo­yl­ov Is­land, Lena Del­ta, Si­be­ria. In­ter­na­tio­nal Mi­cro­bio­lo­gy 11:195–202 (2008).  PubMed  Full Text
Mayr, S., C. Latkoczy, M. Krüger, D. Günther, S. Shima, R.K. Thauer, F. Widdel and B. Jaun: Struc­tu­re of an F430 va­ri­ant from Ar­chaea as­so­cia­ted with an­ae­ro­bic oxi­da­ti­on of me­tha­ne. J. Am. Chem. Soc. 130:10758–10767 (2008).  PubMed
Musat, F., Galushko A., Jacob J., Widde, F., Kube M., Reinhardt R., Wilkes H., Schink B., Rabus R.: An­ae­ro­bic de­gra­da­ti­on of naph­tha­le­ne and 2′me­thyl­naph­tha­le­ne by strains of ma­ri­ne sul­fa­te-re­du­cing bac­te­ria. En­vi­ron. Mi­cro­bi­ol. 11(1):209-219(2008).  PubMed
Musat, F., Widdel F.:  An­ae­ro­bic de­gra­da­ti­on of ben­ze­ne by a ma­ri­ne sul­fa­te-re­du­cing en­rich­ment cul­tu­re, and cell hy­bri­di­za­t­i­on of the do­mi­nant phy­lo­ty­pe. En­vi­ron. Mi­cro­bi­ol. 10(1):10-19 (2008).  PubMed
Scheffel, A., Gärdes A., GrünbergK ., Wanner G. and D. Schüler: The ma­jor ma­gne­to­so­me pro­te­ins MamGFDC are not es­sen­ti­al for ma­gne­ti­te bio­mi­ne­ra­liza­t­i­on in Magnetospirillum gryphiswaldense but re­gu­la­te the size of ma­gne­to­so­me crys­tals. Jour­nal of Bac­te­rio­lo­gy 190(1):377-386 (2008).  PubMed  Full Text
Trautwein, K., Kühner S., Wöhlbrand L., Halder T., Kuchta K., Steinbüchel A., Rabus R.:  Sol­vent stress re­s­pon­se of the de­ni­tri­fy­ing bac­te­ri­um "Aromatoleum aromaticum" strain EbN1. Appl. En­vi­ron. Mi­cro­bi­ol. 74(8):2267-2274 (2008).  PubMed  Full  Text
Widdel, F.:  Er­neu­er­ba­re En­er­gie­trä­ger aus Mi­kro­or­ga­nis­men – Mög­lich­kei­ten und Gren­zen. pp.138-169, An­mer­kun­gen pp.319-323, In:  Die Zu­kunft der En­er­gie.  Gruss, P., Schüth, F. (Hrsg.), C.H. Beck, Mün­chen (2008).
Wöhlbrand, L., Rabus R.:  De­ve­lop­ment of a Ge­ne­tic Sys­tem for the De­ni­tri­fy­ing Bac­te­ri­um 'Aromatoleum aromaticum' Strain EbN1. J. Mol. Mi­cro­bi­ol. Bio­tech­nol. doi: 10.1159/​000159194 (2008).  PubMed
Wöhlbrand, L., Wilkes H., Halder T., Rabus R.:  An­ae­ro­bic de­gra­da­ti­on of p-Ethyl­phe­nol by "Aromatoleum aromaticum" strain EbN1: pa­thway, re­gu­la­ti­on, and in­vol­ved pro­te­ins. J. Bac­te­ri­ol. 190(16):5699-5709 (2008).  PubMed  Full Text
Diploma, M.Sc and B.Sc theses
Appel, Ansgar:  Cha­rac­te­riza­t­i­on of a new, glu­co­se-fer­men­ting ma­ri­ne Gam­ma­pro­te­ob­ac­te­ri­um. Mas­ter the­sis, Uni­ver­si­ty of Os­na­brück (2008).
Czisch, Maik: Cha­rac­te­riza­t­i­on of ma­ri­ne bac­te­ria from the pel­agi­al of the North At­lan­tic (in Ger­man). Di­plo­ma the­sis, Uni­ver­si­ty of Bre­men  (2008).
Dikfidan, Aytac: Es­ta­blish­ment of a ge­ne­tic sys­tem for Castellaniella defragrans Strain 65­Phen (in Ger­man). Di­plo­ma the­sis, Uni­ver­si­tät Bre­men  (2008).
Enning, Dennis: An­ae­ro­bic cor­ro­si­on of iron by cul­tu­res of sulp­ha­te-re­du­cing bac­te­ria. Mas­ter the­sis, Mar­Mic, Uni­ver­si­tät Bre­men, Bre­men (2008).
Gottschall, Matthias:  Op­ti­miza­t­i­on of the pro­te­in pu­ri­fi­ca­ti­on pro­to­col for the iso­la­ti­on of li­n­a­lool-de­hy­dra­ta­se from the de­ni­tri­fy­ing bac­te­ri­um Ca­s­tel­la­ni­el­la de­fra­grans strain 65­Phen (in Ger­man). Di­plo­ma the­sis, Uni­ver­si­ty of Ap­p­lied Sci­en­ces, Jena  (2008).
Holkenbrink, Carina: Ta­xo­no­mi­sche Cha­rak­te­ri­sie­rung von neu­en Spe­zi­es des Ge­nus Rhodopirellula. Ba­che­lor the­sis Uni­ver­si­tät Bre­men, Bre­men (2008).
Jaekel, Ulrike: An­ae­ro­bic oxi­da­ti­on of short-chain and cy­clic al­ka­nes by sulp­ha­te-re­du­cing and de­ni­tri­fy­ing bac­te­ria. Mas­ter the­sis, Mar­Mic, Uni­ver­si­tät Bre­men, Bre­men (2008).
Sommer, Daniel:  Ap­proa­ches to clo­ne and over ex­press two ge­nes from the an­ae­ro­bic mo­no­ter­pe­ne de­gra­da­ti­on pa­thway of Ca­s­tel­la­ni­el­la de­fra­grans 65­Phen.  Ba­che­lor the­sis, Uni­ver­si­ty of Ap­p­lied Sci­en­ces, Bonn-Rhein-Sieg  (2008).
Troppens, Danielle:  Phy­sio­lo­gi­cal cha­rac­te­riza­t­i­on of new­ly iso­la­ted planc­to­my­ce­tes re­sem­bling Rhodopirellula baltica (in Ger­man). Uni­ver­si­ty of Ap­p­lied Sci­en­ces, Ber­lin  (2008).
Uffkes, Judith:  Im­pact of in­crea­sed car­bon di­oxi­de con­cen­tra­ti­on on the struc­tu­re of mi­cro­bi­al com­mu­nities in ma­ri­ne se­di­ments. Di­plo­ma the­sis, Uni­ver­si­ty of Bre­men (2008).
Webner, Kirsten: Ge­n­ex­pres­si­on des an­ae­ro­ben Al­kan­ab­baus in dem de­ni­tri­fi­zie­ren­den Beta­pro­te­ob­ak­te­ri­um OcN1. Mas­ter­ar­beit Uni­ver­si­tät Bre­men, Bre­men (2008).
Wiese, Maria: The fit­ness and for­ma­ti­on of bio­film de­ri­ved va­ri­ants of Serratia marcescens. Di­plom­ar­beit Uni­ver­si­tät Bre­men, Bre­men (2008).
Zaleska, Zane: De­tec­tion of nmsA tran­scripts in naph­tha­le­ne- vs. 2-me­thyl­naph­tha­le­ne-grown cells of the sulp­ha­te-re­du­cing strains NaphS2, NaphS3 and NaphS6. Mas­ter the­sis, Mar­Mic, Uni­ver­si­tät Bre­men, Bre­men (2008).
Ph.D theses
Hoa, Tran Nhu: New or­ga­nic sub­stra­tes for pho­to­tro­phic bac­te­ria. PhD the­sis, Mar­Mic,  Uni­ver­si­tät Bre­men, Bre­men (2008), 104pp.
Junge, Katja: Die Funk­ti­on der CDF-Trans­por­ter MamB und MamM  beim ma­gne­to­so­ma­len Ei­sen­trans­port in Magnetospirillum gryphiswaldense. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2008), 153pp.
Shovitri, Maya: Bac­te­ri­al com­mu­ni­ty in the in­terti­dal se­di­ments po­pu­la­ted by Arenicola marina, a ter­mi­nal re­stric­tion frag­ment length po­ly­mor­phism stu­dy.  Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2008), 135pp.
Wöhlbrand, Lars: Pro­teo­mi­sche und ge­ne­ti­sche Un­ter­su­chun­gen zum Aro­ma­ten-Ab­bau in "Aromatoleum aromaticum" Stamm EbN1. Dis­ser­ta­ti­on Uni­ver­si­tät Bre­men, Bre­men (2008), 213pp.

Di­ver­si­ty Group

Liebner, S., Harder, J.  and Wagner, D.: Bac­te­ri­al di­ver­si­ty and com­mu­ni­ty struc­tu­re in po­ly­go­nal tun­dra soils from Sa­mo­yl­ov Is­land, Lena Del­ta, Si­be­ria. In­ter­na­tio­nal Mi­cro­bio­lo­gy 11:195-202 (2008).  PubMed  Full  Text
Hünken, M., Harder, J.  and Kirst, G.O.: Epi­phytic bac­te­ria on ant­arc­tic ice dia­tom Amphiprora kufferathii Man­gu­in clea­ve hy­dro­gen per­oxi­de pro­du­ced du­ring al­gal pho­to­syn­the­sis.  Plant Bio­lo­gy 10:519-526 (2008).  PubMed
Diploma, M.Sc and B.Sc theses
Appel, Ansgar: Cha­rak­te­ri­sie­rung ei­nes neu­ar­ti­gen, auf Glu­co­se gä­ren­den, ma­ri­nen Gam­ma­pro­te­ob­ak­te­ri­ums. Mas­ter­ar­beit Bio­lo­gie Uni­ver­si­tät Os­na­brück, Os­na­brück (2008), 66pp.
Czisch, Maik: Cha­rak­te­ri­sie­rung von ma­ri­nen Bak­te­ri­en aus dem Pel­agi­al des Nord­at­lan­tiks. Di­plom­ar­beit Bio­lo­gie Uni­ver­si­tät Bre­men, Bre­men (2008), 110pp.
Dikfidan, Aytac: Eta­blie­rung ei­nes ge­ne­ti­schen Sys­tems in Castellaniella defragrans Stamm 65­Phen. Di­plom­ar­beit Bio­lo­gie Uni­ver­si­tät Bre­men, Bre­men (2008), 107pp.
Gottschall, Matthias: Op­ti­mie­rung des Pro­te­in­auf­rei­ni­gungs­pro­to­kolls zur spe­zi­fi­schen Iso­lie­rung der Li­n­a­lool-De­hy­dra­ta­se aus dem ni­tratre­du­zie­ren­den Bak­te­ri­um Castellaniella defragrans Stamm 65­Phen. Di­plom­ar­beit (Dipl.-Ing. (FH) Phar­ma-Bio­tech­no­lo­ge) FH Jena, Jena (2008), 70pp.
Holkenbrink, Carina: Ta­xo­no­mi­sche Cha­rak­te­ri­sie­rung von neu­en Spe­zi­es des Ge­nus Rhodopirellula.  Ba­che­l­or­ar­beit Bio­lo­gie Uni­ver­si­tät Bre­men, Bre­men (2008), 52pp.
Sommer, Daniel: Ap­proa­ches to clo­ne and over­ex­press two ge­nes from the an­ae­ro­bic mo­no­ter­pe­ne de­gra­da­ti­on pa­thway of Castellaniella defragrans 65­Phen.  Ba­che­l­or­ar­beit, Fach­hoch­schu­le Bonn-Rhein-Sieg (2008), 81pp.
Troppens, Danielle: Phy­sio­lo­gi­sche Un­ter­su­chun­gen zur Cha­rak­te­ri­sie­rung von Rhodopirellula baltica ähn­li­chen Planc­to­my­ce­tes-Neui­so­la­ten. Di­plom­ar­beit (Dipl.-Ing. (FH) Bio­tech­no­lo­gie) Tech­ni­sche Fach­hoch­schu­le Ber­lin, Ber­lin (2008), 71pp.

Eco­phy­sio­lo­gy Group

Arning, E. T., D. Birgel, H. N. Schulz-Vogt, L. Holmkvist, B.B. Jørgensen, A. Larson, J. Peckmann: Li­pid bio­mar­ker pat­terns of phos­pho­ge­nic se­di­ments from up­wel­ling re­gi­ons. Geo­mi­cro­bio­lo­gy Jour­nal 25:69-82 (2008).  TFO
Kamp, A., Røy H. and Schulz-Vogt H. N.: Vi­deo-sup­por­ted ana­ly­sis of Beggiatoa fil­ament growth, bre­a­ka­ge, and mo­ve­ment. Mi­cro­bi­al Eco­lo­gy 56:484-491 (2008).  PubMed  Full Text

De­part­ment of Mole­cu­lar Eco­lo­gy

Amann, R. and B. Fuchs: Sin­gle-cell iden­ti­fi­ca­ti­on in mi­cro­bi­al com­mu­nities by im­pro­ved fluo­re­scence in situ hy­bri­di­za­t­i­on tech­ni­ques. Na­tu­re Rev. Mi­cro­bi­ol. 6:339-348 (2008).  PubMed
Allers, E., C. Niesner C. Wild and J. Pernthaler:  Mi­cro­bes en­ri­ched in sea­wa­ter af­ter ad­di­ti­on of co­ral mu­cus. Appl. En­vi­ron. Mi­cro­bi­ol. 74(10):3274-3278 (2008).  PubMed  Full Text
Barberyon, T., F. Carpentier, S. L′Haridon, M. Schüler, G. Michel and R. Amann:  De­scrip­ti­on of Maribacter forsetii sp. nov., a ma­ri­ne Flav­o­bac­te­ri­aceae iso­la­ted from North Sea wa­ter, and emen­ded de­scrip­ti­on of the ge­nus Maribacter. Int. J. Sys­tem. Evol. Mi­cro­bi­ol. 58:790-797 (2008).  PubMed  Full Text
Boetius, A., T. Holler, K. Knittel, J. Felden and F.Wenzhöfer: The se­abed as na­tu­ral la­bo­ra­to­ry: Les­sons from un­cul­ti­va­ted me­tha­notro­phs. pp. 59-82, In: Un­cul­ti­va­ted Mi­cro­or­ga­nisms. Mi­cro­bio­lo­gy Mo­no­graphs,  S. Epstein (ed.), Sprin­ger Ver­lag (2008).  Springer
Gittel, A., M. Mußmann, H. Sass, H. Cypionka, and M. Konneke:  Iden­ti­ty and ab­un­dance of ac­tive sul­fa­te-re­du­cing bac­te­ria in deep ti­d­al flat se­di­ments de­ter­mi­ned by di­rec­ted cul­ti­va­ti­on and CARD-FISH ana­ly­sis. En­vi­ron. Mi­cro­bi­ol. 10(10): 2645-2658 (2008).  PubMed
Hieu, C. X., B. Voigt, D. Albrecht, D. Becher, T. Lombardot, F. O. Glöckner, R. Amann, M. Hecker and T. Schweder:  De­tai­led pro­teo­me ana­ly­sis of gro­wing cells of the planc­to­my­ce­te Rhodopirellula baltica SH1T . Pro­teo­mics 8:1608-1623 (2008).  PubMed
Lösekann, T., A. Robador, H. Niemann, K. Knittel, A. Boetius, and N. Dubilier:  En­do­sym­bio­ses bet­ween bac­te­ria and deep-sea si­bog­li­nid tu­be­worms from an Arc­tic cold seep (Haa­kon Mos­by Mud Vol­ca­no, Ba­rents Sea). En­vi­ron. Mi­cro­bi­ol. 10:3237-3254 (2008).  PubMed
Musat, N., H. Halm, B. Winterholler, P. Hoppe, S. Peduzzi, F. Hillon, F. Horreard, R. Amann, B.B. Jørgensen and M.M.M. Kuypers:  A sin­gle-cell view on the eco­phy­sio­lo­gy of an­ae­ro­bic pho­to­tro­phic bac­te­ria. PNAS 105(46):17861-17866 (2008).  PubMed  Full Text
Payne, M.S., L. Høj, M. Wietz, M.R. Hall, L. Sly and D.G. Bourne: Mi­cro­bi­al di­ver­si­ty of mid-sta­ge Palinurid phyllosoma from Gre­at Bar­ri­er Reef wa­ters. Jour­nal of Ap­p­lied Mi­cro­bio­lo­gy 105:340-350 (2008).  PubMed
Rossel, P.E., J.S. Lipp,  H.F.Fredricks, J. Arnds, A. Boetius, M. Elvert, and K.-U. Hinrichs:  In­tact po­lar li­pids of an­ae­ro­bic me­tha­notro­phic ar­chaea and as­so­cia­ted bac­te­ria. Org. Geo­chem. 39:992-999 (2008).  ScienceDirect
Wegener, G., M. Shovitri, K. Knittel, H. Niemann, M. Hovland, and A. Boetius:  Bio­geo­che­mi­cal pro­ces­ses and mi­cro­bi­al di­ver­si­ty of the Gull­faks and Tom­me­li­ten me­tha­ne seeps (Nort­hern North Sea). Bio­geo­sci­en­ces 5:1127-1144 (2008).  EBSCO
Woebken, D., P. Lam, M.M.M. Kuypers, S.W.A. Naqvi, B. Kartal, M. Strous, M.S.M. Jetten, B.M. Fuchs and R. Amann:  A mi­cro­di­ver­si­ty stu­dy of anam­m­ox bac­te­ria re­veals a no­vel  Can­di­da­tus Scal­in­dua phy­lo­ty­pe in ma­ri­ne oxy­gen mi­ni­mum zo­nes. En­vi­ron. Mi­cro­bi­ol. 10(11):3106-3119 (2008).  PubMed
Yarza, P., M. Richter, J. Peplies, J. Euzeby, R. Amann, K.-H. Schleifer, W. Ludwig, F. O. Glöckner, R. Rosselló-Mora:  The all-spe­cies li­ving tree pro­ject: A 16S rRNA-ba­sed phy­lo­ge­ne­tic tree of all se­quen­ced type strains. Sys­tem. Appl. Mi­cro­bi­ol. 31:241-250 (2008).  PubMed
Zubkov, M.V., G.A. Tarran, I. Mary and B.M. Fuchs: Dif­fe­ren­ti­al mi­cro­bi­al uptake of dis­sol­ved ami­no acids and ami­no su­gars in sur­face wa­ters of the At­lan­tic Oce­an. Jour­nal of Plank­ton Re­se­arch 30(2):211-220 (2008).  JPR  Full Text
Ph.D. theses
Liebner, Susanne: Ad­ap­ti­on, Spa­ti­al Va­ria­bi­li­ty, and Phy­lo­ge­ne­tic Cha­rac­te­riza­t­i­on of Me­tha­notro­phic Com­mu­nities in Per­ma­frost Soils of the Lena Del­ta, Si­be­ria. PhD the­sis, Mar­Mic, Uni­ver­si­tät Bre­men, Bre­men (2008), 119pp.
Richter, Michael: Com­pu­ta­tio­nal Pro­ces­sing and Bio­lo­gi­cal In­ter­pre­ta­ti­on of Ge­no­mes and Me­ta­ge­no­mes of  Ma­ri­ne Bac­te­ria. Dis­ser­ta­ti­on Ja­cobs Uni­ver­si­tät Bre­men, Bre­men (2008), 162pp.

Sym­bio­sis Group

Dubilier, N., Bergin C., Lott C.:  Sym­bio­tic di­ver­si­ty in ma­ri­ne ani­mals: the art of har­n­es­sing che­mo­syn­the­sis. Na­tu­re Re­views Mi­cro­bio­lo­gy 6:725-740 (2008).  PubMed
Lösekann, T., Robador A., Niemann H., Knittel K., Boetius A., Dubilier N.:  En­do­sym­bio­ses bet­ween bac­te­ria and deep-sea si­bog­li­nid tu­be­worms from an Arc­tic cold seep (Haa­kon Mos­by Mud Vol­ca­no, Ba­rents Sea). En­vi­ron. Mi­cro­bi­ol. 10:3237-3254 (2008).  PubMed
Ruehland, C., Blazejak A., Lott C., Loy A., Erséus C., Dubilier N.:  Mul­ti­ple bac­te­ri­al sym­bi­onts in two spe­cies of co-oc­cur­ring gut­less oli­gochae­te worms from Me­di­ter­ra­ne­an sea grass se­di­ments. En­vi­ron. Mi­cro­bi­ol. 10(2):3404-3416 (2008).  PubMed
Martí­nez-Garcí­a, M., Stief P., Dí­az-Valdés M., Wanner G., Ramos-Esplá A., Dubilier N., and Antón J.:  Am­mo­nia-oxi­di­zing Crenarchaeota and ni­tri­fi­ca­ti­on in­si­de the tis­sue of a co­lo­ni­al asci­di­an. En­vi­ron. Mi­cro­bi­ol. 10(11):2991-3001 (2008).  PubMed
M.Sc theses
Fink, Dennis:  Dis­tri­bu­ti­on, ab­un­dance and pro­duc­tivi­ty of en­do­sym­bi­onts in the deep-sea mus­sel Bathymodiolus. Mas­ter the­sis/ PhD The­sis pro­po­sal, Mar­Mic, Uni­ver­si­ty of Bre­men, Bre­men (2008), 55pp.
Röse, Karina: Sym­bio­sis bet­ween bac­te­ria and ba­thy­mo­dio­li­ne mus­sels at hydro­ther­mal vent and cold seep sites. Mas­ter the­sis/ PhD The­sis pro­po­sal, Mar­Mic, Uni­ver­si­ty of Bre­men, Bre­men (2008), 76pp.
Ph.D. thesis
Zielinski, Frank: Geo­bio­lo­gi­cal cou­pling of hydro­ther­mal vent fluids with en­do­sym­bio­tic pri­ma­ry pro­du­cers of Bathymodiolus mus­sels from hydro­ther­mal vents on the Mid-At­lan­tic Ridge. Dis­ser­ta­ti­on, Mar­Mic, Uni­ver­si­ty of Bre­men, Bre­men (2008), 159pp.

Mi­cro­bi­al Ge­no­mics Group

Amaral-Zettler, L., J. Peplies, A. Ramette, B. Fuchs, W. Ludwig and F. O. Glöckner:  Pro­cee­dings of the in­ter­na­tio­nal work­shop on Ri­bo­so­mal RNA tech­no­lo­gy, April 7-9, 2008, Bre­men, Ger­ma­ny. Syst. Appl. Mi­cro­bi­ol. 31:258-268 (2008).  PubMed
Bohnebeck, U., T. Lombardot, R. Kottmann and F. O. Glöckner:  Me­taMi­ne - A tool to de­tect and ana­ly­se gene pat­terns in their en­vi­ron­men­tal con­text. BMC Bio­in­for­ma­tics 9:459, 10pp. (2008).  PubMed  Full Text
Field, D., Garrity, G., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Ashburner, M., Boore, J.L., Cochrane, G., Cole, J., de Pamphilus, C., Edwards, R., Faruque, N., Feldman, R., Gray, T., Gurr, S., Haft, D., Hancock, D., Hertz-Fowler, C., Hughes, J., Joint, I., Kane, M., Kennedy, J., Kolker, E., Kyripides, N., Leebens-Mack, J., Lewis, S., Maltsev, N., Markowitz, V., Methe, B., Morrison, N., Nelson, K., Parkhill, J., Sansone, S., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, T., Turner, S., Ussery, D., Vaughan, B., Whetzel, T., Wilson, G., Wipat, A.: Towards a ri­cher de­scrip­ti­on of our com­ple­te collec­tion of ge­no­mes and me­ta­ge­no­mes: the "Mi­ni­mum In­for­ma­ti­on about a Ge­no­me Se­quence" (MIGS) spe­ci­fi­ca­ti­on. La­wrence Ber­ke­ley Na­tio­nal La­bo­ra­to­ry: La­wrence Ber­ke­ley Na­tio­nal La­bo­ra­to­ry. LBNL Pa­per LBNL-60477, Nat. Bio­tech­nol. 26(5): 541-547 (2008).  IIDI   Full Text
Field, D., F. Oliver Glöckner, G.M. Garrity, T. Gray, P. Sterk, G.Cochrane, R. Vaughan, E. Kolker, R. Kottmann, N. Kyrpides, S. Angiuoli, P. Dawyndt, R.Guralnick, P. Goldstein, N. Hall, L. Hirschman, S. Kravitz, A. L. Lister, V. Markowitz, N. Thomson and T. Whetzel:  Mee­ting re­port: The fourth Ge­no­mic Stan­dards Con­sor­ti­um (GSC) work­shop. Omics 12(2):101-108 (2008).  PubMed  Full  Text
Field, D., G.M. Garrity, S.-A. Sansone, P. Sterk, T. Gray, N. Kyrpides, L. Hirschman, F. Oliver Glöckner, R. Kottmann, S. Angiuoli, O. White, P. Dawyndt, N. Thomson, I.S. Gil, N. Morrison, T. Tatusova, I. Mizrachi, R. Vaughan, G. Cochrane, L. Kagan, S. Murphy, L. Schriml and the Genomic Standards Consortium:  Mee­ting re­port: the fifth Ge­no­mic Stan­dards Con­sor­ti­um (GSC) work­shop. Omics 12(2):109-113 (2008).  PubMed  Full Text
Morrison N. , F.O.Glöckner, R. Kottmann, G. Cochrane, R. Vaughan, G. Garrity, J. Cole, L. Hirschman, L. Schriml, I. Mizrachi, S. Federhen, D. Schindel, S. Miller, P.Hebert, S. Ratnasingham, R. Hanner, L. Amaral-Zettler, M. Sogin, M. Ashburner, S. Lewis, B. Smith, Genomic Standards Consortium (GSC), International Nucleotide Sequence Database Collaboration (INSDC), Consortium for the Barcode of Life (CBOL), International Census of Marine Microbes (ICoMM) and the Environment Ontology Consortium (EnvO): Working to­ge­ther to put mole­cu­les on the map. Na­tu­re 453:978 (2008).  Full Text
Field, D., Morrison N. , F.O. Glöckner, R. Kottmann, G. Cochrane, R. Vaughan, G. Garrity, J. Cole, L. Hirschman, L. Schriml, I. Mizrachi, S. Federhen, D. Schindel, S. Miller, P. Hebert, S. Ratnasingham, R. Hanner, L. Amaral-Zettler, M. Sogin, M. Ashburner, S. Lewis, B. Smith, Genomic Standards Consortium (GSC), International Nucleotide Sequence Database Collaboration (INSDC), Consortium for the Barcode of Life (CBOL), International Census of Marine Microbes (ICoMM) and the Environment Ontology Consortium (EnvO): Working to­ge­ther to put mole­cu­les on the map. Na­tu­re 453:978 (2008).  PubMed
Garrity, G.M. , D. Field, N. Kyrpides, L. Hirschman, S.-A. Sansone, S. Angiuoli, J.R. Cole, F.O. Glöckner, E. Kolker, G. Kowalchuk, M.A. Moran, D. Ussery and O.White:  Toward a stan­dards-com­p­li­ant ge­no­mic and me­ta­ge­no­mic pu­bli­ca­ti­on re­cord. Omics 12(2):157-160 (2008).  PubMed  Full Text
Hieu, C. X., B. Voigt, D. Albrecht, D. Becher, T. Lombardot, F. O. Glöckner, R. Amann, M. Hecker and T. Schweder:  De­tai­led pro­teo­me ana­ly­sis of gro­wing cells of the planc­to­my­ce­te Rhodopirellula baltica SH1T . Pro­teo­mics 8:1608-1623 (2008).  PubMed
Hirschman, L., C. Clark, K. B. Cohen, S. Mardis, J. Luciano, R. Kottmann, J. Cole, V. Markowitz, N. Kyrpides, N. Morrison, L. M. Schriml, D. Field and the Novo Project:  Ha­bi­tat-Lite: A GSC case stu­dy ba­sed on free text terms for en­vi­ron­men­tal me­ta­da­ta. Omics-a Jour­nal of In­te­gra­ti­ve Bio­lo­gy 12:129-136 (2008).  PubMed  Full Text
Kottmann, R., T. Gray, S. Murphy, L. Kagan, S. Kravitz, T. Lombardot, D. Field, F. O. Glöckner and the Genomic Standards Consortium:  A stan­dard MIGS/​MIMS com­p­li­ant XML sche­ma: Toward the de­ve­lop­ment of the Ge­no­mic Con­textu­al Data Mark­up Lan­gua­ge (GCDML). Omics 12(2):115-121 (2008).  PubMed  Full  Text
Peplies, J., R. Kottmann, W. Ludwig and F. O. Glöckner:  A stan­dard ope­ra­ting pro­ce­du­re for phy­lo­ge­ne­tic in­fe­rence (SOP­PI) using (rRNA) mar­ker ge­nes. Syst Appl Mi­cro­bi­ol 31:251-257 (2008).  PubMed
Richter, M., T. Lombardot, I. Kostadinov, R. Kottmann, M. B. Duhaime, J. Peplies and F. O. Glöckner:  JCo­ast - A bio­lo­gist-centric soft­ware tool for data mi­ning and com­pa­ri­son of pro­ka­ryo­tic (meta) ge­no­mes. BMC Bio­in­for­ma­tics 9:177, 9pp. (2008).  PubMed  Full Text
Van Brabant, B., T. Gray, B. Verslyppe, N. Kyrpides, K. Dietrich, F. O. Glöckner, J. Cole, R. Farris, L. M. Schriml, P. De Vos, B. De Baets, D. Field, P. Dawyndt:  Lay­ing the foun­da­ti­on for a ge­no­mic Ro­set­ta sto­ne: Crea­ting in­for­ma­ti­on hubs through the use of con­sen­sus iden­ti­fiers. Omics 12(2):123-127 (2008).  PubMed  Full Text
Yarza, P., M. Richter, J. Peplies, J. Euzeby, R. Amann, K. H. Schleifer, W. Ludwig, F. O. Glöckner and R. Rosselló-Mora.:  The All-Spe­cies Li­ving Tree pro­ject: A 16S rRNA-ba­sed phy­lo­ge­ne­tic tree of all se­quen­ced type strains. Syst Appl Mi­cro­bi­ol 31:241-250 (2008).  PubMed
Diploma and M.Sc theses
Hankeln, Wolfgang:  Me­ta­Bar – a tool for con­sis­tent con­textu­al data ac­qui­si­ti­on for eco­lo­gi­cal ge­no­mics and me­ta­ge­no­mics. Mar­Mic, Mas­ter the­sis,  (2008).
í–ztürk, Basak:  Me­ta­tran­scrip­to­mic ana­ly­sis in the North Sea and the Bal­tic Sea. Mar­Mic, Mas­ter the­sis,  (2008).
Waldmann, Jost:  Phy­lo­print: Ent­wick­lung und An­wen­dung ei­nes Frame­works zur ta­xo­no­mi­schen Klas­si­fi­ka­ti­on. Di­plom­ar­beit (2008).

Nut­ri­ent Group


Duce, R.A., J. LaRoche, K. Altieri, K.R. Arrigo, A.R. Baker, D.G. Capone, S. Cornell, F. Dentener, J. Galloway, R.S. Ganeshram, R.J. Geider, T. Jickells, M.M.M. Kuypers, R. Langlois, P.S. Liss, S.M. Liu, J.J. Middelburg, C.M. Moore, S. Nickovic, A. Oschlies, T. Pedersen, J. Prospero, R. Schlitzer, S. Seitzinger, L.L. Sorensen, M. Uematsu, O. Ulloa, M. Voss, B. Ward, L. Zamora:  Im­pacts of at­mo­s­phe­ric an­thro­po­ge­nic ni­tro­gen on the open oce­an. Sci­ence 320:893-897 (2008).  PubMed
Forster, A., M.M.M. Kuypers, S.C. Turgeon, H.-J. Brumsack, M.R. Petrizzo, J.S. S. Damsté:  The Ce­noma­ni­an/​Turo­ni­an ocea­nic an­oxic event in the South At­lan­tic: New in­sights from a geo­che­mi­cal stu­dy of DSDP Site 530A. Pa­laeo­geo­gra­phy, Pa­laeo­cli­ma­to­lo­gy, Pa­laeo­e­co­lo­gy 267:256–283 (2008).  ScienceDirect
Jensen, M.M., M.M.M. Kuypers, G. Lavik and B. Thamdrup:  Ra­tes and re­gu­la­ti­on of an­ae­ro­bic am­mo­ni­um oxi­da­ti­on and de­ni­tri­fi­ca­ti­on in the Black Sea. Lim­no­lo­gy and Ocea­no­gra­phy 53(1):23-36 (2008).  ASLO  Full Text
Lam P., J. P. Cowen, Popp, B. N. and Jones, R. D.:  Mi­cro­bi­al Am­mo­nia Oxi­da­ti­on and En­han­ced Ni­tro­gen Cy­cling in the En­dea­vour Hydro­ther­mal Plu­me. Geochi­mi­ca et Cos­mochi­mi­ca Acta 72(9): 2268-2286 (2008).  ScienceDirect
Lavik, G., T. Stührmann, V. Brüchert, A. Van der Plas, V. Mohrholz, P. Lam, M. Mußmann, B.M. Fuchs, R. Amann, U. Lass and M.M.M. Kuypers:  De­to­xi­fi­ca­ti­on of sulph­idic Af­ri­can shelf wa­ters by bloo­m­ing che­mo­lit­ho­tro­phs. Na­tu­re 457:581-585 (2008).  PubMed
Musat, N., H. Halm, B. Winterholler, P. Hoppe, S. Peduzzi, F. Hillion, F. Horreard, R. Amann, B.B. Jørgensen and M.M.M. Kuypers:  A sin­gle cell view on the eco­phy­sio­lo­gy of an­ae­ro­bic pho­to­tro­phic bac­te­ria. PNAS 105(46):17861–17866 (2008).  PubMed  Full  Text
Schmid, M.C., A.B. Hooper, M.G. Klotz, D. Woebken, P. Lam, M.M.M. Kuypers, A. Pommerening-Roeser, H.J.M. op den Camp, M.S.M. Jetten:  En­vi­ron­men­tal de­tec­tion of the oc­ta­he­me cycto­chro­me c hy­droxyl­a­mi­ne/​hy­dra­zi­ne ox­ido­re­duc­ta­se ge­nes of ae­ro­bic and an­ae­ro­bic am­mo­ni­um-oxi­di­zing bac­te­ria. En­vi­ron­men­tal Mi­cro­bio­lo­gy 10(11):3140–3149 (2008).  PubMed
Schwermer, C. U., Lavik G., Abed R. M. M., Dunsmore B., Ferdelman T.G., Stoodley P., Gieseke A., de Beer D.: Im­pact of ni­tra­te on the struc­tu­re and func­tion of bac­te­ri­al bio­film com­mu­nities in pipe­lines used for in­jec­tion of sea­wa­ter into oil fiel­ds. Ap­p­lied and En­vi­ron­men­tal Mi­cro­bio­lo­gy 74(9):2841-2851 (2008).  PubMed  Full Text
Woebken, D., P. Lam, M.M.M. Kuypers, S.W.A. Naqvi, B. Kartal, M. Strous, M.S.M. Jetten, B.M. Fuchs and R. Amann:  A mi­cro­di­ver­si­ty stu­dy of anam­m­ox bac­te­ria re­veals a no­vel Can­di­da­tus Scal­in­dua phy­lo­ty­pe in ma­ri­ne oxy­gen mi­ni­mum zo­nes. En­vi­ron­men­tal Mi­cro­bio­lo­gy 10:3106–3119 (2008).  PubMed
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