MarBEF

Chen, S.; Xie, Z.-X.; Yan, K.-Q.; Chen, J.-W.; Li, D.-X.; Wu, P.-F.; Peng, L.; Lin, L.; Dong, C.-M.; Zhao, Z.; Fan, G.-Y.; Liu, S.-Q.; Herndl, G.; Wang, D.-Z. (2024). Functional vertical connectivity of microbial communities in the ocean. Science Advances 10(21): eadj8184. https://dx.doi.org/10.1126/sciadv.adj8184
Fadeev, E.; Hennenfeind, J.H.; Amano, C.; Zhao, Z.; Klun, K.; Herndl, G.; Tinta, T. (2024). Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter. Appl. Environ. Microbiol. 9(2). https://dx.doi.org/10.1128/msystems.01264-23
Masdeu-Navarro, M.; Mangot, J.-F.; Xue, L.; Cabrera-Brufau, M.; Kieber, D.J.; Rodriguez-Ros, P.; Gardner, S.G.; Bergauer, K.; Herndl, G.; Marrasé, C.; Simó, R. (2024). Diel variation of seawater volatile organic compounds, DMSP-related compounds, and microbial plankton inside and outside a tropical coral reef ecosystem. Front. Mar. Sci. 11: 1341619. https://dx.doi.org/10.3389/fmars.2024.1341619
Orel, N.; Fadeev, E.; Herndl, G.J.; Turk, V.; Tinta, T. (2024). Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii. BMC Genom. 25(1). https://dx.doi.org/10.1186/s12864-024-10062-2
Salazar Alekseyeva, K.; Herndl, G.; Baltar, F. (2024). Influence of salinity on the extracellular enzymatic activities of marine pelagic fungi. Journal of Fungi 10(2): 152. https://dx.doi.org/10.3390/jof10020152
Zhao, Z.; Amano, C.; Reinthaler, T.; Orellana, M.V.; Herndl, G. (2024). Substrate uptake patterns shape niche separation in marine prokaryotic microbiome. Science Advances 10(20): eadn5143. https://dx.doi.org/10.1126/sciadv.adn5143
Zhao, Z.; Baltar, F.; Herndl, G. (2024). Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes. Environ. Microbiol. 12(5). https://dx.doi.org/10.1128/spectrum.03036-23
Amano, C.; Reinthaler, T.; Sintes, E.; Varela, M.M.; Stefanschitz, J.; Kaneko, S.; Nakano, Y.; Borchert, W.; Herndl, G.J.; Utsumi, M. (2023). A device for assessing microbial activity under ambient hydrostatic pressure: The in situ microbial incubator (ISMI). Limnol. Oceanogr., Methods 21(2): 69-81. https://dx.doi.org/10.1002/lom3.10528
Baltar, F.; Martínez-Pérez, C.; Amano, C.; Vial, M.; Robaina-Estévez, S.; Reinthaler, T.; Herndl, G.; Zhao, Z.; Logares, R.; Morales, S.E.; González, J.M. (2023). A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean. Nature Microbiology 8(6): 1137-1148. https://dx.doi.org/10.1038/s41564-023-01374-2
Debeljak, P.; Bayer, B.; Sun, Y.; Herndl, G.J.; Obernosterer, I. (2023). Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean. Microbiome 11(1): 187. https://dx.doi.org/10.1186/s40168-023-01600-3
Herndl, G.J.; Bayer, B.; Baltar, F.; Reinthaler, T. (2023). Prokaryotic life in the deep ocean's water column. Ann. Rev. Mar. Sci. 15: 461-483. https://dx.doi.org/10.1146/annurev-marine-032122-115655
Salazar Alekseyeva, K.; Herndl, G.; Baltar, F. (2023). Release of cell-free enzymes by marine pelagic fungal strains. Fungal Biol. 4: 1209265. https://dx.doi.org/10.3389/ffunb.2023.1209265
Srivastava, A.; De Corte, D.; Garcia, J.A.L.; Swan, B.K.; Stepanauskas, R.; Herndl, G.; Sintes, E. (2023). Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses. Environmental Microbiome 11(1): 239. https://dx.doi.org/10.1186/s40168-023-01688-7
Tinta, T.; Zhao, Z.; Bayer, B.; Herndl, G. (2023). Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria. Environmental Microbiome 11(1). https://dx.doi.org/10.1186/s40168-023-01598-8
Amano, C.; Zhao, Z.; Sintes, E.; Reinthaler, T.; Stefanschitz, J.; Kisadur, M.; Utsumi, M.; Herndl, G.J. (2022). Limited carbon cycling due to high-pressure effects on the deep-sea microbiome. Nature Geoscience 15(12): 1041-1047. https://dx.doi.org/10.1038/s41561-022-01081-3
Breyer, E.; Zhao, Z.; Herndl, G.J.; Baltar, F. (2022). Global contribution of pelagic fungi to protein degradation in the ocean. Microbiome 10(1): 143. https://dx.doi.org/10.1186/s40168-022-01329-5
Korlevic, M.; Markovski, M.; Herndl, G.J.; Najdek, M. (2022). Temporal variation in the prokaryotic community of a nearshore marine environment. NPG Scientific Reports 12(1): 16859. https://dx.doi.org/10.1038/s41598-022-20954-6
Malfertheiner, L.; Martínez-Pérez, C.; Zhao, Z.; Herndl, G.J.; Baltar, F. (2022). Phylogeny and metabolic potential of the candidate phylum SAR324. Biology-Basel 11(4): 599. https://dx.doi.org/10.3390/biology11040599
Markovski, M.; Najdek, M.; Herndl, G.J.; Korlevic, M. (2022). Compositional stability of sediment microbial communities during a seagrass meadow decline. Front. Mar. Sci. 9: e966070. https://dx.doi.org/10.3389/fmars.2022.966070
Martínez-Pérez, C.; Greening, C.; Bay, S.K.; Lappan, R.J.; Zhao, Z.; De Corte, D.; Hulbe, C.; Ohneiser, C.; Stevens, C.; Thomson, B.; Stepanauskas, R.; González, J.M.; Logares, R.; Herndl, G.J.; Morales, S.E.; Baltar, F. (2022). Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nature Comm. 13(1): 117. https://dx.doi.org/10.1038/s41467-021-27769-5
Martínez-Pérez, C.; Greening, C.; Bay, S.K.; Lappan, R.J.; Zhao, Z.; De Corte, D.; Hulbe, C.; Ohneiser, C.; Stevens, C.; Thomson, B.; Stepanauskas, R.; González, J.M.; Logares, R.; Herndl, G.J.; Morales, S.E.; Baltar, F. (2022). Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nature Comm. 13(1): 117. https://dx.doi.org/10.1038/s41467-021-27769-5
Munson-McGee, J.H.; Lindsay, M.R.; Sintes, E.; Brown, J.M.; D’Angelo, T.; Brown, J.; Lubelczyk, L.C.; Tomko, P.; Emerson, D.; Orcutt, B.N.; Poulton, N.J.; Herndl, G.J.; Stepanauskas, R. (2022). Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature (Lond.) 712(7941): 764-770. https://dx.doi.org/10.1038/s41586-022-05505-3
Pinto, M.; Zhao, Z.; Klun, K.; Libowitzky, E.; Herndl, G.J. (2022). Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the ocean. mSystems 7(2): e01415-21. https://dx.doi.org/10.1128/msystems.01415-21
Salazar Alekseyeva, K.; Herndl, G.J.; Baltar, F. (2022). Extracellular enzymatic activities of oceanic pelagic fungal strains and the influence of temperature. Journal of Fungi 8(6): 571. https://dx.doi.org/10.3390/jof8060571
Baltar, F.; Alvarez-Salgado, X.A.; Aristegui, J.; Benner, R.; Hansell, D.A.; Herndl, G.J.; Lønborg, C. (2021). What is refractory organic matter in the ocean? Front. Mar. Sci. 8: 642637. https://doi.org/10.3389/fmars.2021.642637
Baltar, F.; Zhao, Z.; Herndl, G.J. (2021). Potential and expression of carbohydrate utilization by marine fungi in the global ocean. Microbiome 9: 106. https://doi.org/10.1186/s40168-021-01063-4
Braun, A.; Spona-Friedl, M.; Avramov, M.; Elsner, M.; Baltar, F.; Reinthaler, T.; Herndl, G.J.; Griebler, C. (2021). Reviews and syntheses: Heterotrophic fixation of inorganic carbon – significant but invisible flux in environmental carbon cycling. Biogeosciences 18(12): 3689-3700. https://dx.doi.org/10.5194/bg-18-3689-2021
De Corte, D.; Muck, S.; Tiroch, J.; Mena, C.; Herndl, G.J.; Sintes, E. (2021). Microbes mediating the sulfur cycle in the Atlantic Ocean and their link to chemolithoautotrophy. Environ. Microbiol. 23(11): 7152-7167. https://dx.doi.org/10.1111/1462-2920.15759
Glatzel, T.; Herndl, G. (2021). Recognizing the complexity of soil organic carbon dynamics in vegetated coastal habitats. Glob. Chang. Biol. 27(1): 3-4. https://doi.org/10.1111/gcb.15426
Jiao, N.; Liu, J.; Edwards, B.; Lv, Z.; Cai, R.; Liu, Y.; Xiao, X.; Wang, J.; Jiao, F.; Wang, R.; Huang, X.; Guo, B.; Sun, J.; Zhang, R.; Zhang, Y.; Tang, K.; Zheng, Q.; Azam, F.; Batt, J.; Cai, W.-J.; He, C.; Herndl, G.J.; Hill, P.; Hutchins, D.; LaRoche, J.; Lewis, M.; MacIntyre, H.; Polimene, L.; Robinson, C.; Shi, Q.; Suttle, C.A.; Thomas, H.; Wallace, D.; Legendre, L. (2021). Correcting a major error in assessing organic carbon pollution in natural waters. Science Advances 7(16): eabc7318. https://doi.org/10.1126/sciadv.abc7318
Korlevic, M.; Markovski, M.; Zhao, Z.; Herndl, G.; Najdek, M. (2021). Seasonal dynamics of epiphytic microbial communities on marine macrophyte surfaces. Front. Microbiol. 12: 671342. https://dx.doi.org/10.3389/fmicb.2021.671342
Korlevic, M.; Markovski, M.; Zhao, Z.; Herndl, G.; Najdek, M. (2021). Selective DNA and protein isolation from marine macrophyte surfaces. Front. Microbiol. 12: 665999. https://dx.doi.org/10.3389/fmicb.2021.665999
Salazar Alekseyeva, K.; Mähnert, B.; Berthiller, F.; Breyer, E.; Herndl, G.J.; Baltar, F. (2021). Adapting an ergosterol extraction method with marine yeasts for the quantification of oceanic fungal biomass. Journal of Fungi 7(9): 690. https://doi.org/10.3390/jof7090690
Srivastava, A.; Saavedra, D.E.M.; Thomson, B.; Garcia, J.A.L.; Zhao, Z.; Patrick, W.M.; Herndl, G.J.; Baltar, F. (2021). Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean. ISME J. 15: 3375-3383. https://doi.org/10.1038/s41396-021-01013-w
Tinta, T.; Klun, K.; Herndl, G.J. (2021). The importance of jellyfish–microbe interactions for biogeochemical cycles in the ocean. Limnol. Oceanogr. 66(5): 2011-2032. https://doi.org/10.1002/lno.11741
Bellou, N.; Garcia, J.A.L.; Colijn, F.; Herndl, G.J. (2020). Seasonality combined with the orientation of surfaces influences the microbial community structure of biofilms in the deep Mediterranean Sea. Deep-Sea Res., Part II, Top. Stud. Oceanogr. 171: 104703. https://dx.doi.org/10.1016/j.dsr2.2019.104703
Chen; Becraft; Pachiadaki, M.; Brown, J.M.; Jarett, J.K.; Gasol, J.M.; Ravin, N.V.; Moser, D.P.; Nunoura, T.; Herndl, G.J.; Woyke, T.; Stepanauskas, R. (2020). Hiding in plain sight: The globally distributed bacterial candidate phylum PAUC34f. Front. Microbiol. 11: article 376. https://dx.doi.org/10.3389/fmicb.2020.00376
Clifford, E.L.; De Corte, D.; Amano, C.; Paliaga, P.; Ivancic, I.; Ortiz, V.; Najdek, M.; Herndl, G.J.; Sintes, E. (2020). Mesozooplankton taurine production and prokaryotic uptake in the northern Adriatic Sea. Limnol. Oceanogr. 65(11): 2730-2747. https://dx.doi.org/10.1002/lno.11544
Mooshammer, M.; Alves, R.J.E.; Bayer, B.; Melcher, M.; Stieglmeier, M.; Jochum, L.; Rittmann, S.K.-M. R.; Watzka, M.; Schleper, C.; Herndl, G.J.; Wanek, W. (2020). Nitrogen isotope fractionation during archaeal ammonia oxidation: Coupled estimates from measurements of residual ammonium and accumulated nitrite. Front. Microbiol. 11: article 1710. https://dx.doi.org/10.3389/fmicb.2020.01710
Najdek, M.; Korlevic, M.; Paliaga, P.; Markovski, M.; Ivancic, I.; Ivesa, L.; Felja, I.; Herndl, G.J. (2020). Dynamics of environmental conditions during the decline of a Cymodocea nodosa meadow. Biogeosciences 17(12): 3299-3315. https://dx.doi.org/10.5194/bg-17-3299-2020
Najdek, M.; Korlevic, M.; Paliaga, P.; Markovski, M.; Ivancic, I.; Ivesa, L.; Felja, I.; Herndl, G.J. (2020). Effects of the invasion of Caulerpa cylindracea in a Cymodocea nodosa meadow in the northern Adriatic Sea. Front. Mar. Sci. 23: 602005. https://doi.org/10.3389/fmars.2020.602055
Pinto, M.; Polania Zenner, P.; Langer, T.M.; Harrison, J.; Simon, M.; Varela, M.M.; Herndl, G.J. (2020). Putative degraders of low‐density polyethylene‐derived compounds are ubiquitous members of plastic‐associated bacterial communities in the marine environment. Environ. Microbiol. 22(11): 4779-4793. https://doi.org/10.1111/1462-2920.15232
Steiner, P.A.; Geijo, J.; Fadeev, E.; Obiol, A.; Sintes, E.; Rattei, T.; Herndl, G.J. (2020). Functional seasonality of free-living and particle-associated prokaryotic communities in the coastal Adriatic Sea. Front. Microbiol. 11: 584222. https://doi.org/10.3389/fmicb.2020.584222
Thomson, B.; Wenley, J.; Lockwood, S.; Twigg, I.; Currie, K.; Herndl, G.J.; Hepburn, C.D.; Baltar, F. (2020). Relative importance of phosphodiesterase vs. phosphomonoesterase (alkaline phosphatase) activities for dissolved organic phosphorus hydrolysis in epi- and mesopelagic waters. Front. Earth Sci. 8: 560893. https://doi.org/10.3389/feart.2020.560893
Tinta, T.; Zhao, Z.; Escobar, A.; Klun, K.; Bayer, B.; Amano, C.; Bamonti, L.; Herndl, G.J. (2020). Microbial processing of jellyfish detritus in the ocean. Front. Microbiol. 11: 590995. https://doi.org/10.3389/fmicb.2020.590995
Weinbauer, M.; Griebler, C.; van Aken, H.M.; Herndl, G. (2020). Viral infection of prokaryotic plankton during early formation of the North Atlantic Deep Water. Aquat. Microb. Ecol. 84: 175-189. https://dx.doi.org/10.3354/ame01934
Zhang, Y.; Qin, W.; Hou, L.; Zakem, E.J.; Wan, X.; Zhao, Z.; Liu, L.; Hunt, K.A.; Jiao, N.; Kao, S.-J.; Tang, K.; Xie, X.; Shen, J.; Li, Y.; Chen, M.; Dai, X.; Liu, C.; Deng, W.; Dai, M.; Ingalls, A.E.; Stahl, D.A.; Herndl, G.J. (2020). Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. Proc. Natl. Acad. Sci. U.S.A. 117(9): 4823-4830. https://dx.doi.org/10.1073/pnas.1912367117
Zhao, Z.; Baltar, F.; Herndl, G. (2020). Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes. Science Advances 6(16): eaaz4354. https://dx.doi.org/10.1126/sciadv.aaz4354
Baltar, F.; Bayer, B.; Bednaršek, N.; Deppeler, S.; Escribano, R.; Gonzalez, C.E.; Hansman, R.L.; Mishra, R.K.; Moran, M.A.; Repeta, D.J. (2019). Towards integrating evolution, metabolism, and climate change studies of marine ecosystems. Trends Ecol. Evol. 34(11): 1022-1033. https://dx.doi.org/10.1016/j.tree.2019.07.003
Baltar, F.; Herndl, G.J. (2019). Ideas and perspectives: Is dark carbon fixation relevant for oceanic primary production estimates? Biogeosciences 16(19): 3793-3799. https://dx.doi.org/10.5194/bg-16-3793-2019
Bayer, B.; Hansman, R.L.; Bittner, M.J.; Noriega-Ortega, B.E.; Niggemann, J.; Dittmar, T.; Herndl, G. (2019). Ammonia‐oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean. Environ. Microbiol. 21(11): 4062-4075. https://dx.doi.org/10.1111/1462-2920.14755
Bayer, B.; Vojvoda, J.; Reinthaler, T.; Reyes, C.; Pinto, M.; Herndl, G.J. (2019). Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria. Int. J. Syst. Evol. Microbiol. 69(7): 1892-1902. https://dx.doi.org/10.1099/ijsem.0.003360
Bayer, B.; Pelikan, C.; Bittner, M.J.; Reinthaler, T.; Könneke, M.; Herndl, G.; Offre, P. (2019). Proteomic response of three marine ammonia-oxidizing archaea to hydrogen peroxide and their metabolic interactions with a heterotrophic alphaproteobacterium. mSystems 4(4): e00181-19. https://dx.doi.org/10.1128/msystems.00181-19
Bochdansky, A.B.; Dunbar, R.B.; Hansell, D.A.; Herndl, G.J. (2019). Estimating carbon flux from optically recording total particle volume at depths below the primary pycnocline. Front. Mar. Sci. 6. https://dx.doi.org/10.3389/fmars.2019.00778
Clifford, E.L.; Varela, M.M.; De Corte, D.; Bode, A.; Ortiz, V.; Herndl, G.J.; Sintes, E. (2019). Taurine is a major carbon and energy source for marine prokaryotes in the North Atlantic Ocean off the Iberian Peninsula. Microb. Ecol. 78(2): 299-312. https://dx.doi.org/10.1007/s00248-019-01320-y
De Corte, D.; Paredes, G.; Yokokawa, T.; Sintes, E.; Herndl, G.J. (2019). Differential response of Cafeteria roenbergensis to different bacterial and archaeal prey characteristics. Microb. Ecol. 78(1): 1-5. https://dx.doi.org/10.1007/s00248-018-1293-y
De Corte, D.; Martinez-Martinez, J.; Cretoiu, M.S.; Takaki, Y.; Nunoura, T.; Sintes, E.; Herndl, G.; Yokokawa, T. (2019). Viral communities in the global deep ocean conveyor belt assessed by targeted viromics. Front. Microbiol. 10: article 1801. https://doi.org/10.3389/fmicb.2019.01801
Köstner, N.; Jürgens, K.; Labrenz, M.; Herndl, G.J.; Winter, C. (2019). Uneven host cell growth causes lysogenic virus induction in the Baltic Sea. PLoS One 14(8): e0220716. https://dx.doi.org/10.1371/journal.pone.0220716
Muck, S.; De Corte, D.; Clifford, E.L.; Bayer, B.; Herndl, G.J.; Sintes, E. (2019). Niche differentiation of aerobic and anaerobic ammonia oxidizers in a high latitude deep oxygen minimum zone. Front. Microbiol. 10: article 2141. https://dx.doi.org/10.3389/fmicb.2019.02141
Pinto, M.; Langer, T.M.; Hüffer, T.; Hofmann, T.; Herndl, G.J. (2019). The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession. PLoS One 14(6): e0217165. https://dx.doi.org/10.1371/journal.pone.0217165
Steiner, P.A.; Sintes, E.; Simó, R.; De Corte, D.; Pfannkuchen, D.M.; Ivancic, I.; Najdek, M.; Herndl, G.J. (2019). Seasonal dynamics of marine snow‐associated and free‐living demethylating bacterial communities in the coastal northern Adriatic Sea. Environmental Microbiology Reports 11(5): 699-707. https://dx.doi.org/10.1111/1758-2229.12783
Steiner, P.A.; De Corte, D.; Geijo, J.; Mena, C.; Yokokawa, T.; Rattei, T.; Herndl, G.J.; Sintes, E. (2019). Highly variable mRNA half‐life time within marine bacterial taxa and functional genes. Environ. Microbiol. 21(10): 3873-3884. https://dx.doi.org/10.1111/1462-2920.14737
Thomson, B.; Wenley, J.; Currie, K.; Hepburn, C.; Herndl, G.J.; Baltar, F. (2019). Resolving the paradox: Continuous cell-free alkaline phosphatase activity despite high phosphate concentrations. Mar. Chem. 214: 103671. https://dx.doi.org/10.1016/j.marchem.2019.103671
Tinta, T.; Kogovsek, T.; Klun, K.; Malej, A.; Herndl, G.J.; Turk, V. (2019). Jellyfish-associated microbiome in the marine environment: exploring its biotechnological potential. Mar. Drugs 17(2): 94. https://dx.doi.org/10.3390/md17020094
Bergauer, K.; Fernàndez-Guerra, A.; Garcia, J.A.L.; Sprenger, R.R.; Stepanauskas, R.; Pachiadaki, M.G.; Jensen, O.N.; Herndl, G. (2018). Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proc. Natl. Acad. Sci. U.S.A. 115(3): E400-E408. https://dx.doi.org/10.1073/pnas.1708779115
De Corte, D.; Srivastava, A.; Koski, M.; Garcia, J.A.L.; Takaki, Y.; Yokokawa, T.; Elisabeth, N.H.; Nunoura, T.; Sintes, E.; Herndl, G.J. (2018). Metagenomic insights into zooplankton-associated bacterial communities. Environ. Microbiol. 20(2): 492-505. https://dx.doi.org/10.1111/1462-2920.13944
Engelen, A.H.; Aires, T.; Vermeij, M.J.A.; Herndl, G.J.; Serrão, E.A.; Frade, P.R. (2018). Host differentiation and compartmentalization of microbial communities in the azooxanthellate cupcorals Tubastrea coccinea and Rhizopsammia goesi in the Caribbean. Front. Mar. Sci. 5: 391. https://dx.doi.org/10.3389/fmars.2018.00391
Guerrero-Feijóo, E.; Sintes, E.; Herndl, G.J.; Varela, M.M. (2018). High dark inorganic carbon fixation rates by specific microbial groups in the Atlantic off the Galician coast (NW Iberian margin). Environ. Microbiol. 20(2): 602-611. https://dx.doi.org/10.1111/1462-2920.13984
Ivancic, I.; Paliaga, P.; Pfannkuchen, M.; Djakovac, T.; Najdek, M.; Steiner, P.; Korlevic, M.; Markovski, M.; Baricevic, A.; Tankovic, M.S.; Herndl, G. (2018). Seasonal variations in extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water. FEMS Microbiol. Ecol. 94(12): 11. https://doi.org/10.1093/femsec/fiy198
Romera-Castillo, C.; Pinto, M.; Langer, T.M.; Alvarez-Salgado, X.A.; Herndl, G. (2018). Dissolved organic carbon leaching from plastics stimulates microbial activity in the ocean. Nature Comm. 9(1): 7 pp. https://dx.doi.org/10.1038/s41467-018-03798-5
Clifford, E.L.; Hansell, D.A.; Varela, M.M.; Nieto-Cid, M.; Herndl, G.J.; Sintes, E. (2017). Crustacean zooplankton release copious amounts of dissolved organic matter as taurine in the ocean. Limnol. Oceanogr. 62(6): 2745-2758. https://dx.doi.org/10.1002/lno.10603
Debeljak, P.; Proietti, M.; Reisser, J.; Ferrari, F.F.; Abbas, B.; van Loosdrecht, M.C.M.; Slat, B.; Herndl, G.J. (2017). Extracting DNA from ocean microplastics: a method comparison study. Anal. Methods 9(9): 1521-1526. https://dx.doi.org/10.1039/C6AY03119F
Elling, F.J.; Könneke, M.; Nicol, G.W.; Stieglmeier, M.; Bayer, B.; Spieck, E.; de la Torre, J.R.; Becker, K.W.; Thomm, M.; Prosser, J.I.; Herndl, G.J.; Schleper, C.; Hinrichs, K.-U. (2017). Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ. Microbiol. 19(7): 2681-2700. https://doi.org/10.1111/1462-2920.13759
Glasl, B.; Bongaerts, P.; Elisabeth, N.H.; Hoegh-Guldberg, O.; Herndl, G.J.; Frade, P.R. (2017). Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m). Coral Reefs 36(2): 447-452. https://dx.doi.org/10.1007/s00338-016-1517-x
Köstner, N.; Scharnreitner, L.; Jürgens, K.; Labrenz, M.; Herndl, G.J.; Winter, C. (2017). High viral abundance as a consequence of low viral decay in the Baltic Sea redoxcline. PLoS One 12(6): e0178467. https://dx.doi.org/10.1371/journal.pone.0178467
Landry, Z.; Swan, B.K.; Herndl, G.J.; Stepanauskas, R.; Giovannonia, S.J. (2017). SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation ofRecalcitrant Dissolved Organic Matter. Mbio 8(2): e00413-17. https://dx.doi.org/10.1128/mBio.00413-17
Pachiadaki, M.G.; Sintes, E.; Bergauer, K.; Brown, J.M.; Record, N.R.; Swan, B.K.; Mathyer, M.E.; Hallam, S.J.; López-Garcìa, P.; Takaki, Y.; Nunoura, T.; Woyke, T.; Herndl, G.J.; Stepanauskas, R. (2017). Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science (Wash.) 358(6366): 1046-1051. https://dx.doi.org/10.1126/science.aan8260
Baltar, F.; Lundin, D.; Palovaara, J.; Lekunberri, I.; Reinthaler, T.; Herndl, G.; Pinhassi, J. (2016). Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO₂ Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic. Front. Microbiol. 7: 1670. dx.doi.org/10.3389/fmicb.2016.01670
Bayer, B.; Vojvoda, J.; Offre, P.; Alves, R.J.E.; Elisabeth, N.H.; Garcia, J.A.L.; Volland, J.-M.; Srivastava, A.; Schleper, C.; Herndl, G. (2016). Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. ISME J. 10: 1051-1063. dx.doi.org/10.1038/ismej.2015.200
Bochdansky, A.B.; Clouse, M.A.; Herndl, G. (2016). Dragon kings of the deep sea: marine particles deviate markedly from the common number-size spectrum. NPG Scientific Reports 6(22633): 7 pp. http://dx.doi.org/10.1038/srep22633
De Corte, D.; Sintes, E.; Yokokawa, T.; Lekunberri, I.; Herndl, G. (2016). Large-scale distribution of microbial and viral populations in the South Atlantic Ocean. Environmental Microbiology Reports 8(2): 305-315. dx.doi.org/10.1111/1758-2229.12381
Frade, P.R.; Schwaninger, V.; Glasl, B.; Sintes, E.; Hill, R.W.; Simó, R.; Herndl, G. (2016). Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus. Environ. Chem. 13: 252–265. dx.doi.org/10.1071/EN15023
Frade, P.R.; Roll, K.; Bergauer, K.; Herndl, G. (2016). Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs. PLoS One 11(1): e0144702. dx.doi.org/10.1371/journal.pone.0144702
Frank, A.H.; Garcia, J.A.L.; Herndl, G.; Reinthaler, T. (2016). Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water. Environ. Microbiol. 18(6): 2052–2063. dx.doi.org/10.1111/1462-2920.13237
Frank, A.H.; Pontiller, B.; Herndl, G.; Reinthaler, T. (2016). Erythromycin and GC7 fail as domain-specific inhibitors for bacterial and archaeal activity in the open ocean . Aquat. Microb. Ecol. 77: 99-110. dx.doi.org/10.3354/ame01792
Glasl, B.; Herndl, G.; Frade, P.R. (2016). The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance. ISME J. 10: 2280–2292. dx.doi.org/10.1038/ismej.2016.9
Piquet, A.M.-T.; Maat, D.S.; Confurius-Guns, V.; Sintes, E.; Herndl, G.; van de Poll, W.H.; Wiencke, C.; Buma, A.G.J.; Bolhuis, H. (2016). Springtime dynamics, productivity and activity of prokaryotes in two Arctic fjords. Polar Biol. 39: 1749–1763. dx.doi.org/10.1007/s00300-015-1866-x
Sintes, E.; De Corte, D.; Haberleitner, E.; Herndl, G. (2016). Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean. Front. Microbiol. 7: 77. dx.doi.org/10.3389/fmicb.2016.00077
Arrieta, J.M.; Mayol, E.; Hansman, R.L.; Herndl, G.J.; Dittmar, T.; Duarte, C.M. (2015). Dilution limits dissolved organic carbon utilization in the deep ocean. Science (Wash.) 348(6232): 331-333. http://dx.doi.org/10.1126/science.1258955
Arrieta, J.M.; Mayol, E.; Hansman, R.L.; Herndl, G.J.; Dittmar, T.; Duarte, C.M. (2015). Response to Comment on "Dilution limits dissolved organic carbon utilization in the deep ocean". Science (Wash.) 350(6267): 1483-1483. http://dx.doi.org/10.1126/science.aac7249
Hansman, R.L.; Dittmar, T.; Herndl, G.J. (2015). Conservation of dissolved organic matter molecular composition during mixing of the deep water masses of the northeast Atlantic Ocean. Mar. Chem. 177: 288–297. dx.doi.org/10.1016/j.marchem.2015.06.001
Malits, A.; Cattaneo, R.; Sintes, E.; Gasol, J.M.; Herndl, G.J.; Weinbauer, M.G. (2015). Potential impacts of black carbon on the marine microbial community. Aquat. Microb. Ecol. 75: 27-42. dx.doi.org/10.3354/ame01742
Sintes, E.; Ouillon, N.; Herndl, G.J. (2015). Macroecological patterns of archaeal ammonia oxidizers in the Atlantic Ocean. Mol. Ecol. 24: 4931–4942 . dx.doi.org/10.1111/mec.13365
De Corte, D.; Lekunberri, I.; Sintes, E.; Garcia, J.A.L.; Gonzalez, S.; Herndl, G.J. (2014). Linkage between copepods and bacteria in the North Atlantic Ocean. Aquat. Microb. Ecol. 72: 215-225. http://dx.doi.org/10.3354/ame01696
Muck, S.; Griessler, T.; Köstner, N.; Klimiuk, A.; Winter, C.; Herndl, G.J. (2014). Fracture zones in the Mid Atlantic Ridge lead to alterations in prokaryotic and viral parameters in deep-water masses. Front. Microbiol. 5: 264. http://dx.doi.org/10.3389/fmicb.2014.00264
Winter, C.; Garcia, J.A.L.; Weinbauer, M.G.; DuBow, M.S.; Herndl, G.J. (2014). Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea. PLoS One 9(6): e100600 1-8. http://dx.doi.org/10.1371/journal.pone.0100600
Zhang, Y.; Zhao, Z.; Dai, M.; Jiao, N.; Herndl, G.J. (2014). Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea. Mol. Ecol. 23(9): 2260-2274. dx.doi.org/10.1111/mec.12739
Assmy, P.; Smetacek, V.; Klaas, C.; Henjes, J.; Strass, V.H.; Arrieta, J.M.; Bathmann, U.; Cisewski, B.; Fuchs, N.; Herndl, G.J. (2013). Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current. Proc. Natl. Acad. Sci. U.S.A. 110(51): 20633–20638. http://dx.doi.org/10.1073/pnas.1309345110
Baltar, F.; Arístegui, J.; Gasol, J.M.; Yokokawa, T.; Herndl, G.J. (2013). Bacterial Versus Archaeal Origin of Extracellular Enzymatic Activity in the Northeast Atlantic Deep Waters. Microb. Ecol. 65(2): 277-288. dx.doi.org/10.1007/s00248-012-0126-7
Baltar, F.; Reinthaler, T.; Herndl, G.J.; Pinhassi, J. (2013). Major Effect of Hydrogen Peroxide on Bacterioplankton Metabolism in the Northeast Atlantic. PLoS One 8(4). dx.doi.org/10.1371/journal.pone.0061051
Bergauer, K.; Sintes, E.; van Bleijswijk, J.; Witte, H.; Herndl, G.J. (2013). Abundance and distribution of archaeal acetyl-CoA/propionyl-CoA carboxylase genes indicative for putatively chemoautotrophic Archaea in the tropical Atlantic's interior. FEMS Microbiol. Ecol. 84(3): 461-473. dx.doi.org/10.1111/1574-6941.12073
Calleja, M.L.; Duarte, C.M.; Álvarez, M.; Vaquer-Sunyer, R.; Agustí, S.; Herndl, G.J. (2013). Prevalence of strong vertical CO₂ and O₂ variability in the top meters of the ocean. Global Biogeochem. Cycles 27: 941–949. http://dx.doi.org/10.1002/gbc.20081
De Corte, D.; Sintes, E.; Yokokawa, T.; Herndl, G.; De Corte, D. (2013). Comparison between MICRO-CARD-FISH and 16S rRNA gene clone libraries toassess the active versus total bacterial community in the coastal Arctic. Environmental Microbiology Reports 5(2): 272-281. dx.doi.org/10.1111/1758-2229.12013
Herndl, G.J.; Reinthaler, T. (2013). Microbial control of the dark end of the biological pump. Nature Geoscience 6(9): 718-724. dx.doi.org/10.1038/NGEO1921
Lekunberri, I.; Sintes, E.; de Corte, D.; Yokokawa, T.; Herndl, G.J. (2013). Spatial patterns of bacterial and archaeal communities along the Romanche Fracture Zone (tropical Atlantic). FEMS Microbiol. Ecol. 85(3): 537-552. dx.doi.org/10.1111/1574-6941.12142
Reinthaler, T.; Herndl, G.J.; Álvarez-Salgado, X.A.; Álvarez, M.; van Aken, H.M. (2013). Impact of water mass mixing on the biogeochemistry and microbiology of the Northeast Atlantic Deep Water. Global Biogeochem. Cycles 27(4): 1151–1162. http://dx.doi.org/10.1002/2013GB004634
Sintes, E.; Witte, H.; Stodderegger, K.; Steiner, P.; Herndl, G.J. (2013). Temporal dynamics in the free-living bacterial community composition in the coastal North Sea. FEMS Microbiol. Ecol. 83(2): 413-424. dx.doi.org/10.1111/1574-6941.12003
Baltar, F.; Aristegui, J.; Gasol, J.M.; Herndl, G.J. (2012). Microbial Functioning and Community Structure Variability in the Mesopelagic and Epipelagic Waters of the Subtropical Northeast Atlantic Ocean. Appl. Environ. Microbiol. 78(9): 3309-3316. dx.doi.org/10.1128/AEM.07962-11
De Corte, D.; Sintes, E.; Yokokawa, T.; Reinthaler, T.; Herndl, G.J. (2012). Links between viruses and prokaryotes throughout the water column along a North Atlantic latitudinal transect. ISME J. 6(8): 1566-1577. dx.doi.org/10.1038/ismej.2011.214
Smetacek, V.; Klaas, C.; Strass, V.H.; Assmy, P.; Montresor, M.; Cisewski, B.; Savoye, N.; Webb, A.; d'Ovidio, F.; Arrieta, J.M.; Bathmann, U.; Bellerby, R.; Berg, G.M.; Croot, P.; Gonzalez, S.; Henjes, J.; Herndl, G.J.; Hoffmann, L.J.; Leach, H.; Losch, M.; Mills, M.M.; Neill, C.; Peeken, I.; Röttgers, R.; Sachs, O.; Sauter, E.; Schmidt, M.M.; Schwarz, J.; Terbrüggen, A.; Wolf-Gladrow, D. (2012). Deep carbon export from a Southern Ocean iron-fertilized diatom bloom. Nature (Lond.) 487(7407): 313-319. https://dx.doi.org/10.1038/nature11229
Thomas, H.; Craig, S.E.; Greenan, B.J.W.; Burt, W.; Herndl, G.J.; Higginson, S.; Salt, L.; Shadwick, E.H.; Urrego-Blanco, J. (2012). Direct observations of diel biological CO₂ fixation on the Scotian Shelf, northwestern Atlantic Ocean. Biogeosciences 9(6): 2301-2309. dx.doi.org/10.5194/bg-9-2301-2012
Yokokawa, T.; Sintes, E.; de Corte, D.; Olbrich, K.; Herndl, G.J. (2012). Differentiating leucine incorporation of Archaea and Bacteria throughout the water column of the eastern Atlantic using metabolic inhibitors. Aquat. Microb. Ecol. 66(3): 247-256. dx.doi.org/10.3354/ame01575
Agogue, H.; Lamy, D.; Neal, P.R.; Sogin, M.L.; Herndl, G.J. (2011). Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Mol. Ecol. 20(2): 258-274. dx.doi.org/10.1111/j.1365-294X.2010.04932.x
de Corte, D.; Sintes, E.; Yokokawa, T.; Herndl, G.J.; de Corte, D. (2011). Changes in viral and bacterial communities during the ice-melting season in the coastal Arctic (Kongsfjorden, Ny-Ålesund). Environ. Microbiol. 13(7): 1827-1841. dx.doi.org/10.1111/j.1462-2920.2011.02497.x
Llabres, M.; Agustí, S.; Herndl, G.J. (2011). Diel in situ picophytoplankton cell death cycles coupled with cell division. J. Phycol. 47(6): 1247-1257. dx.doi.org/10.1111/j.1529-8817.2011.01072.x
Morgan-Smith, D.; Herndl, G.J.; van Aken, H.M.; Bochdansky, A.B. (2011). Abundance of eukaryotic microbes in the deep subtropical North Atlantic. Aquat. Microb. Ecol. 65(2): 103-115. dx.doi.org/10.3354/ame01536
Muia, A.W.; Bretschko, G.; Herndl, G.J. (2011). An overview of the structure and function of microbial biofilms, withspecial emphasis on heterotrophic aquatic microbial communities. Afr. J. Aquat. Sci. 36(1): 1-10. dx.doi.org/10.2989/16085914.2011.562279
Varela, M.M.; van Aken, H.M.; Sintes, E.; Reinthaler, T.; Herndl, G.J. (2011). Contribution of Crenarchaeota and Bacteria to autotrophy in the North Atlantic interior. Environ. Microbiol. 13(6): 1524-1533. dx.doi.org/10.1111/j.1462-2920.2011.02457.x
Llabrés, M.; Agusti, S.; Alonso-Laita, P.; Herndl, G.J. (2010). Synechococcus and Prochlorococcus cell death induced by UV radiation and the penetration of lethal UVR in the Mediterranean Sea. Mar. Ecol. Prog. Ser. 399: 27-37. http://dx.doi.org/10.3354/meps08332
Agogué, H.; Brink, M.; Herndl, G.J. (2008). Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature (Lond.) 456(7223): 788-791
Parada, V.; Herndl, G.J.; Weinbauer, M.G. (2006). Viral burst size of heterotrophic prokaryotes in aquatic systems. J. Mar. Biol. Ass. U.K. 86(3): 613-621. https://dx.doi.org/10.1017/S002531540601352X

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