Baltar, F, Arístegui, J, Montero, MF, Espino, M, Gasol, JM & Herndl, G 2009, 'Mesoscale variability modulates seasonal changes in the trophic structure of nano- and picoplankton communities across the NW Africa-Canary Islands transition zone' Progress in Oceanography, vol 83, no. 180-188.

Herndl, G 2009, 'Microbial oceanography of the dark ocean's pelagic realm.' Limnology and Oceanography, pp. 1501-1529.

Aristegui, J, Gasol, JM, Duarte, CM & Herndl, G 2009, 'Microbial oceanography of the dark ocean’s pelagic realm' Limnology and Oceanography, vol 54, no. 1501-1529.

Herndl, G 2009, 'Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic.' Environmental Microbiology, pp. 1998-2014.

Herndl, G 2009, 'Role of mesoscale cyclonic eddies in the distribution and activity of Archaea and Bacteria in the South China Sea.' Aquatic Microbial Ecology, vol 56, pp. 65-79.

Winter, C, Weinbauer, M & Kerros, M-E 2009, 'Seasonal and depth-related dynamics of prokaryotes and viruses in surface and deep waters of the northwestern Mediterranean Sea.' Deep-Sea Research. Part 1: Oceanographic Research Papers, vol 56, pp. 1972-1982.

Winter, C, Weinbauer, M & Kerros, M-E 2009, 'Seasonal changes of bacterial and archaeal communities in the dark ocean:Evidence from the Mediterranean Sea.' Limnology and Oceanography, vol 54, no. 1, pp. 160-170.

Herndl, G 2009, 'Spatial distribution of Bacteria and Archaea and amo A gene copy numbers throughout the water column of the eastern Mediterranean Sea.' The ISME Journal: multidisciplinary journal of microbial ecology, vol 3, no. 2, pp. 147-158.

De Corte, D, Yokokawa, T, Varela, MM, Agogué, H & Herndl, G 2009, 'Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the eastern Mediterranean Sea' The ISME Journal: multidisciplinary journal of microbial ecology, vol 3, no. 147,158.

Herndl, G 2009, 'Viral and flagellate control of prokaryotic production and community structure in offshore Mediterranean waters.' Applied and Environmental Microbiology, vol 75, no. 14, pp. 4801-4812. DOI: 10.1128/AEM.01376-08

Wangberg, S-A, Andreasson, KIM, Gustavson, K, Reinthaler, T & Henriksen, P 2008, 'UV-B effects on microplankton communities in Kongsfjord, Svalbard - A mesocosm experiment' Journal of Experimental Marine Biology and Ecology, vol 365, no. 2, pp. 156-163. DOI: 10.1016/j.jembe.2008.08.010

Winter, C, Moeseneder, MM, Herndl, GJ & Weinbauer, MG 2008, 'Relationship of geographic distance, depth, temperature, and viruses with prokaryotic communities in the eastern tropical Atlantic Ocean' Microbial Ecology: an international journal, vol 56, no. 2, pp. 383-389. DOI: 10.1007/s00248-007-9343-x

Stoica, E & Herndl, GJ 2008, 'Contribution of Crenarchaeota and Euryarchaeota to the prokaryotic plankton in the coastal northwestern Black Sea (vol 29, pg 699, 2008)' Journal of Plankton Research, vol 30, no. 1, pp. 93-93. DOI: 10.1093/plankt/fbm081

Reinthaler, T, Sintes Elvelin, E & Herndl, GJ 2008, 'Dissolved organic matter and bacterial production and respiration in the sea-surface microlayer of the open Atlantic and the western Mediterranean Sea' Limnology and Oceanography, vol 53, no. 1, pp. 122-136.

Varela, MM, van Aken, HM & Herndl, G 2008, 'Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic' Environmental Microbiology, vol 10, no. 1903-1911.

Parada, V, Baudoux, A-C, Sintes Elvelin, E, Weinbauer, MG & Herndl, G 2008, 'Dynamics and diversity of newly produced virioplankton in the North Sea' The ISME Journal: multidisciplinary journal of microbial ecology, vol 2, no. 924-936.

Herndl, G, Labrenz, M, Grote, J & Jürgens, K 2008, 'Epsilonproteobacteria represent the major portion of chemoautotrophic bacteria in sulfidic waters of pelagic redoxclines of the Baltic and Black Seas.' Applied and Environmental Microbiology, vol 74, no. 24, pp. 7546-7551. DOI: 10.1128/AEM.01186-08

Varela, MM, van Aken, HM, Sintes Elvelin, E & Herndl, G 2008, 'Latitudinal trends of Crenarchaeota and Bacteria in the meso- and bathypelagic water masses of the North Atlantic' Environmental Microbiology, vol 10, no. 110-124.

Agogué, H, Brink, M, Dinasquet, J & Herndl, G 2008, 'Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic' Nature, vol 456, pp. 788-791.

Herndl, GJ, Agogue, H, Baltar, F, Reinthaler, T, Sintes Elvelin, E & Varela, MM 2008, 'Regulation of aquatic microbial processes: the A 'microbial loop' of the sunlit surface waters and the dark ocean dissected' Aquatic Microbial Ecology, vol 53, no. 1, pp. 59-68. DOI: 10.3354/ame01225