In the context of global change, marine organisms are subjected not only to gradual changes in abiotic parameters, but also to an increasing number of extreme events, such as heatwaves. However, we still know little about the influence of heatwaves on the structure of marine communities, and experimental studies are needed to test the impact of heatwaves alone and in combination with other environmental drivers. Here, we condu...

Summary Marine heterotrophic bacteria contribute considerably to global carbon cycling, in part by utilizing phytoplankton‐derived polysaccharides. The patterns and rates of two different polysaccharide utilization modes – extracellular hydrolysis and selfish uptake – have previously been found to change during spring phytoplankton bloom events. Here we investigated seasonal changes in bacterial utilization of three polysaccha...

Summary Microbial communities have important functions during spring phytoplankton blooms, regulating bloom dynamics and processing organic matter. Despite extensive research into such processes, an in‐depth assessment of the fungal component is missing, especially for the smaller size fractions. We investigated the dynamics of unicellular mycoplankton during a spring phytoplankton bloom in the North Sea by 18S rRNA gene tag s...

Summary Spring phytoplankton blooms in temperate environments contribute disproportionately to global marine productivity. Bloom‐derived organic matter, much of it occurring as polysaccharides, fuels biogeochemical cycles driven by interacting autotrophic and heterotrophic communities. We tracked changes in the mode of polysaccharide utilization by heterotrophic bacteria during the course of a diatom‐dominated bloom in the Ger...

Summary The N 2 ‐fixing (diazotrophic) community in marine ecosystems is dominated by non‐cyanobacterial microorganisms. Yet, very little is known about their identity, function and ecological relevance due to a lack of cultured representatives. Here we report a novel heterotrophic diazotroph isolated from the oxygen minimum zone (OMZ) off Peru. The new species belongs to the genus Sagittula ( Rhodobacteraceae , Alphaproteobac...

Summary Gammaproteobacterial Reinekea spp. were detected during North Sea spring algae blooms in the years 2009‐2012, with relative abundances of up to 16% in the bacterioplankton. Here, we explore the ecophysiology of ‘R. forsetii' strain Hel1_31_D35 that was isolated during the 2010 spring bloom using (i) its manually annotated, high‐quality closed genome, (ii) re‐analysis of in situ data from the 2009–2012 blooms and (iii)...

Summary Although fluorescence in situ hybridization (FISH) with specific ribosomal RNA (rRNA)‐targeted oligonucleotides is a standard method to detect and identify microorganisms, the specific detection of genes in bacteria and archaea, for example by using geneFISH, requires complicated and lengthy (> 30 h) procedures. Here we report a much improved protocol, direct‐geneFISH, which allows specific gene and rRNA detection with...

The Po River runoff strongly affects the oceanographic and ecological characteristics of the Northern Adriatic Sea. Catalysed reported deposition ‐ fluorescence in situ hybridization ( CARD ‐ FISH ) analysis was employed to assess how the composition of the coastal bacterioplankton community is influenced by the river runoff in two different seasons (spring and autumn). Samples were collected from the water column along a coas...

Summary Marine Bacteroidetes have pronounced capabilities of degrading high molecular weight organic matter such as proteins and polysaccharides. Previously we reported on 76 Bacteroidetes ‐affiliated fosmids from the North Atlantic Ocean's boreal polar and oligotrophic subtropical provinces. Here, we report on the analysis of further 174 fosmids from the same libraries. The combined, re‐assembled dataset (226 contigs; 8.8 Mbp...

Summary The C hlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small pl...

Summary Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in‐situ hybridization and pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and coastal marine particles > 5 and > 10 μm respectively. Limnic particles were more abundant (average: 1 × 10 7 l −1 ), smaller in si...

Summary The roles of individual bacterioplankton species in the re‐mineralization of algal biomass are poorly understood. Evidence from molecular data had indicated that a spring diatom bloom in the G erman B ight of the N orth S ea in 2009 was followed by a rapid succession of uncultivated bacterioplankton species, including members of the genera U lvibacter , F ormosa , P olaribacter (class F lavobacteria ) and R einekea (cl...

Summary The globally abundant, uncultured unicellular cyanobacterium UCYN ‐ A was recently discovered living in association with a eukaryotic cell closely related to a prymnesiophyte. Here, we established a double CAtalysed Reporter Deposition‐Fluorescence In Situ Hybridization ( CARD ‐ FISH ) approach to identify both partners and provided quantitative information on their distribution and abundance across distinct water mass...

Summary Magnetotactic bacteria ( MTB ), which orient along the earth's magnetic field using magnetosomes, are ubiquitous and abundant in marine and freshwater environments. Previous phylogenetic analysis of diverse MTB has been limited to few cultured species and the most abundant and conspicuous members of natural populations, which were assigned to various lineages of the P roteobacteria , the N itrospirae phylum as well as...

Summary Bacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean, the Polar Biome (BPLR)...

Summary Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, su...

Summary Members of the prokaryotic picoplankton are the main drivers of the biogeochemical cycles over large areas of the world's oceans. In order to ascertain changes in picoplankton composition in the euphotic and twilight zones at an ocean basin scale we determined the distribution of 11 marine bacterial and archaeal phyla in three different water layers along a transect across the Atlantic Ocean from South Africa (32.9°S)...