Gunnar Gerdts

Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom.

Blooming Succession Algal blooms in the ocean will trigger a succession of microbial predators and scavengers. Teeling et al. (p. 608) used a combination of microscopy, metagenomics, and metaproteomics to analyze samples from a North Sea diatom bloom over time. Distinct steps of polysaccharide degradation and carbohydrate uptake could be assigned to clades of Flavobacteria and Gammaproteobacteria, which differ profoundly in their transporter profiles and their uptake systems for phosphorus. The phytoplankton/bacterioplankton coupling in coastal marine systems is of crucial importance for global carbon cycling. Bacterioplankton clade succession following phytoplankton blooms may be predictable enough that it can be included in models of global carbon cycling. Seasonal diatom growth in the North Sea results in a temporal succession of metabolically specialized bacteria. Phytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession of populations at genus-level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes (transporters; in particular, TonB-dependent transporters) and phosphate acquisition strategies were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria are specialized for successive decomposition of algal-derived organic matter. Our results suggest that algal substrate availability provided a series of ecological niches in which specialized populations could bloom. This reveals how planktonic species, despite their seemingly homogeneous habitat, can evade extinction by direct competition.

Isolation of Novel Pelagic Bacteria from the German Bight and Their Seasonal Contributions to Surface Picoplankton

ABSTRACT We tested new strategies for the isolation of abundant bacteria from coastal North Sea surface waters, which included reducing by several orders of magnitude the concentrations of inorganic N and P compounds in a synthetic seawater medium. Agar plates were resampled over 37 days, and slowly growing colonies were allowed to develop by repeatedly removing all newly formed colonies. A fivefold increase of colonies was observed on plates with reduced nutrient levels, and the phylogenetic composition of the culture collection changed over time, towards members of the Roseobacter lineage and other alpha-proteobacteria. Novel gamma-proteobacteria from a previously uncultured but cosmopolitan lineage (NOR5) formed colonies only after 12 days of plate incubation. A time series of German Bight surface waters (January to December 1998) was screened by fluorescence in situ hybridization (FISH) with isolate-specific and general probes. During spring and early summer, a prominent fraction of FISH-detectable bacteria (mean, 51%) were affiliated with theCytophaga-Flavobacterium group (CF) of theBacteroidetes. One Cytophaga sp. lineage with cultured representatives formed almost 20% of the CF group. Members of the Roseobacter cluster constituted approximately 50% of alpha-proteobacteria, but none of the Roseobacter-related isolates formed populations of >1% in the environment. Thus, the readily culturable members of this clade are probably not representative of Roseobacter species that are common in the water column. In contrast, members of NOR5 were found at high abundances (>105 cells ml−1) in the summer plankton. Some abundant pelagic bacteria are apparently able to form colonies on solid media, but appropriate isolation techniques for different species need to be developed.

The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.

Dinoroseobacter shibae DFL12T, a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12T is able to synthesize the vitamins B1 and B12 for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B12 are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B12 was confirmed to be functional, and D. shibae DFL12T was shown to provide the growth-limiting vitamins B1 and B12 to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12T is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12T has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12T shows the most complex viral defense system of all Rhodobacterales sequenced to date.

Plastic ingestion by pelagic and demersal fish from the North Sea and Baltic Sea

Plastic ingestion by marine biota has been reported for a variety of different taxa. In this study, we investigated 290 gastrointestinal tracts of demersal (cod, dab and flounder) and pelagic fish species (herring and mackerel) from the North and Baltic Sea for the occurrence of plastic ingestion. In 5.5% of all investigated fishes, plastic particles were detected, with 74% of all particles being in the microplastic (<5mm) size range. The polymer types of all found particles were analysed by means of Fourier transform infrared (FT-IR) spectroscopy. Almost 40% of the particles consisted of polyethylene (PE). In 3.4% of the demersal and 10.7% of the pelagic individuals, plastic ingestion was recorded, showing a significantly higher ingestion frequency in the pelagic feeders. The condition factor K was calculated to test differences in the fitness status between individuals with and without ingested plastic, but no direct effect was detected.

Methodology Used for the Detection and Identification of Microplastics—A Critical Appraisal

Microplastics in aquatic ecosystems and especially in the marine environment represent a pollution of increasing scientific and societal concern, thus, recently a substantial number of studies on microplastics were published. Although first steps towards a standardization of methodologies used for the detection and identification of microplastics in environmental samples are made, the comparability of data on microplastics is currently hampered by a huge variety of different methodologies, which result in the generation of data of extremely different quality and resolution. This chapter reviews the methodology presently used for assessing the concentration of microplastics in the marine environment with a focus on the most convenient techniques and approaches. After an overview of non-selective sampling approaches, sample processing and treatment in the laboratory, the reader is introduced to the currently applied techniques for the identification and quantification of microplastics. The subsequent case study on microplastics in sediment samples from the North Sea measured with focal plane array (FPA)-based micro-Fourier transform infrared (micro-FTIR) spectroscopy shows that only 1.4 % of the particles visually resembling microplastics were of synthetic polymer origin. This finding emphasizes the importance of verifying the synthetic polymer origin of potential microplastics. Thus, a burning issue concerning current microplastic research is the generation of standards that allow for the assessment of reliable data on concentrations of microscopic plastic particles and the involved polymers with analytical laboratory techniques such as micro-FTIR or micro-Raman spectroscopy.

Small changes in pH have direct effects on marine bacterial community composition: a microcosm approach

As the atmospheric CO2 concentration rises, more CO2 will dissolve in the oceans, leading to a reduction in pH. Effects of ocean acidification on bacterial communities have mainly been studied in biologically complex systems, in which indirect effects, mediated through food web interactions, come into play. These approaches come close to nature but suffer from low replication and neglect seasonality. To comprehensively investigate direct pH effects, we conducted highly-replicated laboratory acidification experiments with the natural bacterial community from Helgoland Roads (North Sea). Seasonal variability was accounted for by repeating the experiment four times (spring, summer, autumn, winter). Three dilution approaches were used to select for different ecological strategies, i.e. fast-growing or low-nutrient adapted bacteria. The pH levels investigated were in situ seawater pH (8.15–8.22), pH 7.82 and pH 7.67, representing the present-day situation and two acidification scenarios projected for the North Sea for the year 2100. In all seasons, both automated ribosomal intergenic spacer analysis and 16S ribosomal amplicon pyrosequencing revealed pH-dependent community shifts for two of the dilution approaches. Bacteria susceptible to changes in pH were different members of Gammaproteobacteria, Flavobacteriaceae, Rhodobacteraceae, Campylobacteraceae and further less abundant groups. Their specific response to reduced pH was often context-dependent. Bacterial abundance was not influenced by pH. Our findings suggest that already moderate changes in pH have the potential to cause compositional shifts, depending on the community assembly and environmental factors. By identifying pH-susceptible groups, this study provides insights for more directed, in-depth community analyses in large-scale and long-term experiments.

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. We investigated such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down to the genus level. Metagenome analyses also revealed recurrent patterns at the functional level, in particular with respect to algal polysaccharide degradation genes. We, therefore, hypothesize that even though there is substantial inter-annual variation between spring phytoplankton blooms, the accompanying succession of bacterial clades is largely governed by deterministic principles such as substrate-induced forcing. DOI: http://dx.doi.org/10.7554/eLife.11888.001

Microplastic concentrations in beach sediments along the German Baltic coast

The contamination with microplastic particles and fibres was evaluated on beaches along the German Baltic coast. Sediments were sampled near the Warnow and Oder/Peene estuaries, on Rügen island and along the Rostock coast to derive possible entry pathways. Seasonal variations were monitored along the Rostock coast from March to July 2014. After density separation in saline solution, floating particles were found to be dominated by sand grains. Water surface tension is shown to be sufficient to explain floatation of grains with sizes less than 1.5mm. Selecting intensely coloured particles and fibres, we find lower limits of the microplastic concentrations of 0-7 particles/kg and 2-11 fibres/kg dry sediment. The largest microplastic contaminations are measured at the Peene outlet into the Baltic Sea and in the North Sea Jade Bay. City discharges, industrial production sites, fishing activity and tourism are the most likely sources for the highest microplastic concentrations.

Focal plane array detector-based micro-Fourier-transform infrared imaging for the analysis of microplastics in environmental samples

The pollution of the environment with microplastics (plastic pieces ,5 mm) is a problem of increasing concern. However, although this has been generally recognised by scientists and authorities, the analysis of microplastics is often done by visual inspection alone with potentially high error rates, especially for smaller particles. Methods that allow for a fast and reliable analysis of microplastics enriched on filters are lacking. Our study is the first to fill this gap by using focal plane array detector-based micro-Fourier-transform infrared imaging for analysis of microplastics from environmental samples. As a result of ouriteratively optimised analytical approach (concerningfilter material, measuring mode, measurement parameters and identification protocol), we were able to successfully measure the whole surface (>10-mm diameter) of filters with microplastics from marine plankton and sediment samples. The measurement with a highlateralresolutionallowedforthedetectionofparticlesdowntoasizeof20mminonlyafractionalpartoftimeneeded for chemical mapping. The integration of three band regions facilitated the pre-selection of potential microplastics of the ten most important polymers. Subsequent to the imaging the review of the infrared spectra of the pre-selected potential microplastics wasnecessaryforaverificationofplastic polymerorigin.Theapproachwepresenthereishighlysuitableto be implemented as a standard procedure for the analysis of small microplastics from environmental samples. However, a further automatisation with respect to measurement and subsequent particle identification would facilitate the even faster and fully automated analysis of microplastic samples. Additional keywords: microplastic analysis, microplastic detection, microplastic identification.

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters

Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type.