The results of empirical studies have revealed links between phytoplankton and bacterioplankton, such as the frequent correlation between chlorophyll a and bulk bacterial abundance and production. Nevertheless, little is known about possible links at the level of specific taxonomic groups. To investigate this issue, seawater microcosm experiments were performed in the northwestern Mediterranean Sea. Turbulence was used as a noninvasive means to induce phytoplankton blooms dominated by different algae. Microcosms exposed to turbulence became dominated by diatoms, while small phytoflagellates gained importance under still conditions. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments showed that changes in phytoplankton community composition were followed by shifts in bacterioplankton community composition, both as changes in the presence or absence of distinct bacterial phylotypes and as differences in the relative abundance of ubiquitous phylotypes. Sequencing of DGGE bands showed that four Roseobacter phylotypes were present in all microcosms. The microcosms with a higher proportion of phytoflagellates were characterized by four phylotypes of the Bacteroidetes phylum: two affiliated with the family Cryomorphaceae and two with the family Flavobacteriaceae . Two other Flavobacteriaceae phylotypes were characteristic of the diatom-dominated microcosms, together with one Alphaproteobacteria phylotype ( Roseobacter ) and one Gammaproteobacteria phylotype ( Methylophaga ). Phylogenetic analyses of published Bacteroidetes 16S rRNA gene sequences confirmed that members of the Flavobacteriaceae are remarkably responsive to phytoplankton blooms, indicating these bacteria could be particularly important in the processing of organic matter during such events. Our data suggest that quantitative and qualitative differences in phytoplankton species composition may lead to pronounced differences in bacterioplankton species composition.

Significance: Prokaryotes dominate the living biomass and the biological diversity of the ocean, one of the largest ecosystems on earth. The sinking of particles is a widespread mechanism that transports materials to the deep ocean, with a significant role in the global carbon cycle. Whether this process constitutes a global dispersal pathway for prokaryotic diversity connecting surface communities to those in the dark ocean has never been tested. Here we show that surface and deep-sea prokaryotic communities are strongly connected, constituting a vast oceanic metacommunity where local assemblages are linked through the transport of sinking particles. This vertical dispersal, mediated mainly by the largest sinking particles, emerges as a fundamental process shaping the assembly and biogeography of deep ocean prokaryotic communities.

12 pages, 5 figures, 2 tablesBacterioplankton growth is expected to depend on the availability of organic and inorganic nutrients. Still, no studies have investigated how the magnitude and type of nutrient limitation experienced by marine bacteria change on a temporal scale. We carried out a series of nutrient enrichment experiments to examine the variability in nutrient limitation of bacteria in the NW Mediterranean Sea, at monthly intervals, over an 18 mo period. Short-term enrichment bioassays (24 h incubation) showed that bacterial P limitation could occur throughout the year, but was most pronounced during spring and summer, coinciding with very low concentrations of dissolved inorganic phosphorus and chlorophyll a, and higher N:P ratios. During the non-stratified period in autumn and winter, bacteria were at times strongly C limited. Inorganic nitrogen limitation was not detected at any time. Long-term bioassays with and without enrichment, where growth was monitored until stationary phase using the seawater dilution culture approach, largely confirmed the results from the short-term bioassays. Analysis of the bacterial assemblages in these cultures, using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene sequencing, suggested that the growth of some central components of the native bacterioplankton assemblage (i.e. specific Roseobacter and Flavobacteria phylotypes) was restricted due to the limited availability of P in spring and summer. We conclude that seasonal variability in the type and severity of nutrient limitation can substantially contribute to the regulation of bacterioplankton growth and community composition, and thereby affect the turnover of dissolved organic matter and inorganic nutrients in the seaThis work was supported by the Swedish Science Council (project 621-2003-2692, to J.P.), and the Spanish MCyT projects MicroDiff (REN2001-2120/MAR) and MODIVUS (CTM2005-04795/MAR), and the EU project BASICS (EVK3-CT-2002-00078) to J.M.G.Peer reviewe

Depending on their relationship with the pelagic particulate matter, planktonic prokaryotes have traditionally been classified into two types of communities: free-living (FL) or attached (ATT) to particles, and are generally separated using only one pore-size filter in a differential filtration. Nonetheless, particulate matter in the oceans appears in a continuum of sizes. Here we separated this continuum into six discrete size-fractions, from 0.2 to 200 μm, and described the prokaryotes associated to each of them. Each size-fraction presented different bacterial communities, with a range of 23–42% of unique (OTUs) in each size-fraction, supporting the idea that they contained distinct types of particles. An increase in richness was observed from the smallest to the largest size-fractions, suggesting that increasingly larger particles contributed new niches. Our results show that a multiple size-fractionation provides a more exhaustive description of the bacterial diversity and community structure than the use of only one filter. In addition, and based on our results, we propose an alternative to the dichotomy of FL or ATT lifestyles, in which we differentiate the taxonomic groups with preference for the smaller fractions, those that do not show preferences for small or large fractions, and those that preferentially appear in larger fractions.

We investigated the effects of an increase in dissolved CO₂ on the microbial communities of the Mediterranean Sea during two mesocosm experiments in two contrasting seasons: winter, at the peak of the annual phytoplankton bloom, and summer, under low nutrient conditions. The experiments included treatments with acidification and nutrient addition, and combinations of the two. We followed the effects of ocean acidification (OA) on the abundance of the main groups of microorganisms (diatoms, dinoflagellates, nanoeukaryotes, picoeukaryotes, cyanobacteria, and heterotrophic bacteria) and on bacterial activity, leucine incorporation, and extracellular enzyme activity. Our results showed a clear stimulation effect of OA on the abundance of small phytoplankton (pico- and nanoeukaryotes), independently of the season and nutrient availability. A large number of the measured variables showed significant positive effects of acidification in summer compared with winter, when the effects were sometimes negative. Effects of OA were more conspicuous when nutrient concentrations were low. Our results therefore suggest that microbial communities in oligotrophic waters are considerably affected by OA, whereas microbes in more productive waters are less affected. The overall enhancing effect of acidification on eukaryotic pico- and nanophytoplankton, in comparison with the non-significant or even negative response to nutrient-rich conditions of larger groups and autotrophic prokaryotes, suggests a shift towards medium-sized producers in a future acidified ocean.