Occurrence of cyanobacterial blooms in the baltic sea in relation to environmental conditions

Cyanobacterial blooms occur regularly in summer in central parts of the Baltic Sea. They are mainly composed of Aphanizomenon sp. and Nodularia spumigena. Both species have almost similar ecological requirements and can roughly be considered a uniform functional group. In order to identify factors that might favour bloom development, water quality data from monitoring programmes were compared with bloom distribution. A salinity from 3.8 to 11.5 PSU proved important for the spatial distribution of the bloom development. The bloom's onset was triggered by temperatures approximating 16°C provided that global radiation was > 120 W/m² (daily mean) and wind speed was < 6 m/s. Nutrient concentrations decreased immediately before the bloom. The bloom's development ceased with poor weather conditions characterized by low irradiation or high wind speed.     

Flocculation of microalgae in brackish and sea waters

Flocculation is an essential step in the concentration and harvesting of microalgae from aquatic media. Salinity of brackish water and sea water requires high flocculant dosages and renders flocculation less effective than in freshwater algal media. Experiments with the marine microalgae Isochrysis galbana and Chlorella stigmatophora showed that effective alum or ferric chloride flocculation was obtained only with dosages which are 5 to 10 times higher than the dosages required for the flocculation of freshwater microalgae. The flocculant dosages required for removing over 90% of the algae from suspensions were found to increase linearly with salinity as expressed in ionic strength. High salinity was found to inhibit flocculation with polyelectrolytes which are quite effective in freshwater algae flocculation. This inhibition was diminished at reduced salinity levels and effective flocculation was attained at salinity levels of 5 g/liter and below, which is typical of desert brackish water. Two methods were found to induce flocculation in sea water: (a) combining polyelectrolytes with inorganic flocculants such as ferric chloride or alum, and (b) ozone oxidation pretreatment followed by flocculation with inorganic flocculants.     

Distribution of the uncultured protist MAST-4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real-time quantitative PCR

Molecular surveys of marine picoeukaryotes have revealed a large number of sequences unrelated to cultured organisms, such as those forming the marine stramenopile (MAST)-4 clade. Recent FISH (fluorescent in situ hybridization) data have shown that MAST-4 cells are uncultured heterotrophic flagellates of 2–3 μm in size that have a global distribution in non-polar marine waters. However, FISH is time-consuming and hard to apply to the many samples generated during oceanographic cruises, so we developed a real-time quantitative polymerase chain reaction (Q-PCR) protocol to determine rapidly the abundance of this group using environmental DNA. We designed a primer set targeting the 18S rRNA genes (rDNA) of MAST-4 and optimized and calibrated the Q-PCR protocol using a plasmid with the target sequence as insert. The Q-PCR was then applied to quantify MAST-4 rDNA molecules along three marine transects, longitudinal in the Indian Ocean, latitudinal in the Drake Passage and coastal–offshore in the Mediterranean Sea, and to a temporal study in a Mediterranean Sea coastal station. MAST-4 was detected in all samples processed (averaged abundances between 500 and 1000 rDNA molecules ml⁻¹) except in mesopelagic and Antarctic samples, where it was virtually absent. In general, it was more abundant in the coast than offshore and in the deep chlorophyll maximum than at surface. A comparison of Q-PCR and FISH signals in well-controlled microbial incubations indicated that MAST-4 cells have around 30 copies of the rDNA operon. This Q-PCR assay quickly yielded quantitative data of uncultured MAST-4 cells and confirmed their wide distribution and putative ecological importance.     

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

With the advent of molecular methods, it became clear that microbial biodiversity had been vastly underestimated. Since then, species abundance patterns were determined for several environments, but temporal changes in species composition were not studied to the same level of resolution. Using massively parallel sequencing on the 454 GS FLX platform we identified a highly dynamic turnover of the seasonal abundance of protists in the Austrian lake Fuschlsee. We show that seasonal abundance patterns of protists closely match their biogeographic distribution. The stable predominance of few highly abundant taxa, which previously led to the suggestion of a low global protist species richness, is contrasted by a highly dynamic turnover of rare species. We suggest that differential seasonality of rare and abundant protist taxa explains the—so far—conflicting evidence in the ‘everything is everywhere’ dispute. Consequently temporal sampling is basic for adequate diversity and species richness estimates.     

Decadal-scale changes of dinoflagellates and diatoms in the anomalous baltic sea spring bloom

The algal spring bloom in the Baltic Sea represents an anomaly from the winter-spring bloom patterns worldwide in terms of frequent and recurring dominance of dinoflagellates over diatoms. Analysis of approximately 3500 spring bloom samples from the Baltic Sea monitoring programs revealed (i) that within the major basins the proportion of dinoflagellates varied from 0.1 (Kattegat) to >0.8 (central Baltic Proper), and (ii) substantial shifts (e.g. from 0.2 to 0.6 in the Gulf of Finland) in the dinoflagellate proportion over four decades. During a recent decade (1995-2004) the proportion of dinoflagellates increased relative to diatoms mostly in the northernmost basins (Gulf of Bothnia, from 0.1 to 0.4) and in the Gulf of Finland, (0.4 to 0.6) which are typically ice-covered areas. We hypothesize that in coastal areas a specific sequence of seasonal events, involving wintertime mixing and resuspension of benthic cysts, followed by proliferation in stratified thin layers under melting ice, favors successful seeding and accumulation of dense dinoflagellate populations over diatoms. This head-start of dinoflagellates by the onset of the spring bloom is decisive for successful competition with the faster growing diatoms. Massive cyst formation and spreading of cyst beds fuel the expanding and ever larger dinoflagellate blooms in the relatively shallow coastal waters. Shifts in the dominant spring bloom algal groups can have significant effects on major elemental fluxes and functioning of the Baltic Sea ecosystem, but also in the vast shelves and estuaries at high latitudes, where ice-associated cold-water dinoflagellates successfully compete with diatoms.     

Unveiling protein functions through the dynamics of the interaction network

Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.     

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable-isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the ¹³C-DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non-culturable microorganisms by combining both SIP and metagenome binning.     

High turnover of fungal hyphae in incubation experiments

Soil biological studies are often conducted on sieved soils without the presence of plants. However, soil fungi build delicate mycelial networks, often symbiotically associated with plant roots (mycorrhizal fungi). We hypothesized that as a result of sieving and incubating without plants, the total fungal biomass decreases. To test this, we conducted three incubation experiments. We expected total and arbuscular mycorrhizal (AM) fungal biomass to be higher in less fertilized soils than in fertilized soils, and thus to decrease more during incubation. Indeed, we found that fungal biomass decreased rapidly in the less fertilized soils. A shift towards thicker hyphae occurred, and the fraction of septate hyphae increased. However, analyses of phospholipid fatty acids (PLFAs) and neutral lipid fatty acids could not clarify which fungal groups were decreasing. We propose that in our soils, there was a fraction of fungal biomass that was sensitive to fertilization and disturbance (sieving, followed by incubation without plants) with a very high turnover (possibly composed of fine hyphae of AM and saprotrophic fungi), and a fraction that was much less vulnerable with a low turnover (composed of saprotrophic fungi and runner hyphae of AMF). Furthermore, PLFAs might not be as sensitive in detecting changes in fungal biomass as previously thought.     

Seasonal fluctuations in macrobenthic fauna of theFucus belt in kiel fjord (western baltic sea)

The macrobenthic fauna associated withFucus at a station in the Kiel Fjord was investigated from June 1978 until June 1979. The predominant group in number as well as in biomass were gammarids. They formed, together with the isopodsIdotea spp., approximately 95 % of the total average annual biomass. The total dry weight of all macrobenthic animals (excl.Littorina spp.) increased from 1.9 g per kgFucus in May to about 16 g in June–August, and dropped to 8.3 g in September. Winter average dry weight values were only about 6 % of the summer values.     

rRNA and rDNA based assessment of sea ice protist biodiversity from the central Arctic Ocean

Sea ice is a large and diverse ecosystem contributing significantly to primary production in ice-covered regions. In the Arctic Ocean, sea ice consists of mixed multi-year ice (MYI), often several metres thick, and thinner first-year ice (FYI). Current global warming is most severe in Arctic regions; as a consequence, summer sea ice cover is decreasing and MYI is disappearing at an alarming rate. Despite its apparent hostility, sea ice is inhabited by a diverse microbial community of bacteria and protists, many of which are photosynthetic. Here we present an assessment of eukaryotic biodiversity in MYI and FYI from the central Arctic Ocean using high-throughput 454 sequencing of 18S rRNA and rDNA amplicons. We compared the rDNA-based ‘total’ biodiversity with the ‘active’ biodiversity from rRNA amplicons and found differences between them including an over-representation of Ciliophora, Bicosoecida and Bacillariophyceae operational taxonomic units (OTUs) in the active part of the community. Differences between the two libraries are more pronounced at the lower taxonomic level: certain genera, such as Melosira, are more abundant in the rRNA library, indicating activity of these genera. Furthermore, we found that one FYI station showed a higher activity of potential grazers which was probably due to the advanced stage of melt evident by higher ice temperatures and highly porous ice compared with the other stations.     

Unveiling functions of the visual cortex using task-specific deep neural networks

The human visual cortex enables visual perception through a cascade of hierarchical computations in cortical regions with distinct functionalities. Here, we introduce an AI-driven approach to discover the functional mapping of the visual cortex. We related human brain responses to scene images measured with functional MRI (fMRI) systematically to a diverse set of deep neural networks (DNNs) optimized to perform different scene perception tasks. We found a structured mapping between DNN tasks and brain regions along the ventral and dorsal visual streams. Low-level visual tasks mapped onto early brain regions, 3-dimensional scene perception tasks mapped onto the dorsal stream, and semantic tasks mapped onto the ventral stream. This mapping was of high fidelity, with more than 60% of the explainable variance in nine key regions being explained. Together, our results provide a novel functional mapping of the human visual cortex and demonstrate the power of the computational approach.     

Survival and growth of sea trout parr in fresh and brackish water

There was no di.erence in survival or growth rate over 63 days for young-of-the-year sea trout Salmo trutta in fresh and brackish Baltic Sea water (6·7 psu). Hence, such sea trout parr that migrate from the freshwater habitat in which they hatch to the Baltic coastal zone, without smolting, should experience little or no physiological cost in survival and growth.     

On the potential of fatty acids as trophic markers in Arctic grazers: feeding experiments with sea urchins and amphipods fed nine diets of macroalgae

To elucidate dietary preferences of benthic grazers at the Arctic Kongsfjorden by means of fatty acid trophic markers, ten different parallel treatments (starvation, 3 species of red macroalgae, 4 species of brown macroalgae and 2 species of green macroalgae) were offered as mono-algal diet to specimens of the dominant sea urchin Strongylocentrotus droebachiensis (Echinodermata, Echinoidea) and the gammarid amphipod Gammarellus homari (Crustacea, Amphipoda). At the end of the 3-week feeding experiments, amphipods and sea urchins (soft tissue) were deep-frozen and analysed for total lipid contents as well as fatty acid (FA) compositions. In addition, FA profiles of the algal species were determined and screened for specific FA patterns or single FAs qualifying as potential trophic markers in the grazers. Despite their diets of nine algal species with different FA compositions, FA patterns of the sea urchins and amphipods revealed a pronounced similarity between treatments. This strong similarity was also observed in the faecal pellets of the sea urchins. Hence, deviating FA compositions of the macroalgae were neither reflected in the FA patterns of the grazers’ tissue nor in their faecal pellets. Suitable algal FA trophic markers could thus not be identified in the two grazers from Kongsfjorden. The rather low lipid levels, especially in the amphipods, as well as a pronounced degradation and modification of FAs may explain that the FA trophic marker approach did not provide evidence of dietary preferences. Future experiments may obtain a higher resolution of potential FA trophic markers by analysing separate lipid classes or single tissues of lipid-poor grazers. Alternatively, different methods are needed to reveal high-resolution trophic relationships between macroalgae and herbivores in Kongsfjorden.     

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant–mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil–plant continuums (rhizosphere, phyllosphere and endosphere) in the maize–wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop-associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub-community is mainly determined by stochastic processes. In contrast, the rare sub-community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co-occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions.     

Feasibility of incubation experiments to estimate moulting rates in marine copepods

Moulting rate estimates of Temora longicornis and Pseudocalanuselongatus in short incubation experiments in the laboratorywere compared with shipboard experiments in the North Sea. Absenceof food, rotation of bottles and (an extremely small) containersize did not affect the moulting rate in well-fed copepods.A minor bias was found due to gentle handling. High variancewas due to the use of different samples, one before and oneafter incubation, which is part of the so-called ‘Kimmerermethod’. This error can be reduced by monitoring the newproduction of exuviae in a single sample, which makes sortingof individuals unnecessary, while conserving the estimate ofmoulting rate in individual stages.     

Nutrient enrichment experiments in three central Florida lakes of different trophic states

Seasonal nutrient enrichment experiments (short-term bioassays) were conducted in three Florida lakes of different trophic states to determine the effects of addition of various nutrient combinations upon chlorophyll a and phytoplankton standing crops. Nutrient enriched surface water samples with crustacean zooplankton removed were incubated in situ in clear polyethylene bags for 3 to 6 days. The 2⁵ factorial design employed two levels (ambient and enriched) of each of five nutrients [NH₄ ⁺, PO _inf4 ^sup3− , Fe⁻ -EDTA, SiO _inf3 ^sup2− and a cation (Ca²⁺ or K⁺) or trace elements]. Ammonium produced significant increases in chlorophyll a and phytoplankton standing crops in all experiments. Phosphate produced similar results in the mesotrophic lake, but the eutrophic lakes had both positive and nonsignificant responses which varied seasonally between lakes. Iron increased chlorophyll a in most experiments but affected total phytoplankton standing crop only during the summer and fall. Silicon had negative effects in some experiments. Cations and trace elements produced marked differences between lakes for chlorophyll a, but total phytoplankton standing crop showed few significant responses. Synergistic responses to two- and three-factor interactions were observed in all lakes. Differences in the responses of phytoplankton taxonomic divisions to enrichment may be responsible for much of the between lake variation in chlorophyll a and total phytoplankton volume responses. Nutrient limitations in these lakes are discussed and related to limnological factors and predictive models.