Identification of the heterotrophic nanoflagellate Bilabrum latius in the southern Adriatic (Mediterranean Sea)

Heterotrophic flagellates (HF) represent an important protist group in marine ecosystem functioning. Characterised by high taxonomic diversity, identification and classification of HF is often difficult using classical methods of light microscopy (LM). Complementing LM with molecular methods, such as barcoding, enables reliable taxonomic identification of even small size nanoflagellates that share similar or unnoticeable morphological features. The order Bicosoecida is a group of heterotrophic nanoflagellates that are important part of protist plankton and benthic communities of the world oceans. Recently, on the basis of high-resolution light microscopy and barcoding, a new bicosoecid genus, Bilabrum, was described with B. latius sp. as a type species. Our study reports on identification of B. latius from co-culture with the diatom species Chaetoceros affinis isolated from fresh plankton samples collected in the southern Adriatic. This detection of the Adriatic B.latius represents first record of this species outside itś up to now known and described habitat (deep-sea sediment of the South - East Atlantic Ocean) and in diatom co-culture.

Recommendations for the preservation of environmental samples in diatom metabarcoding studies

Implementation of DNA metabarcoding for diatoms for environmental monitoring is now moving from a research to an operational phase, requiring rigorous guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies and now need to be rationalised. The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design used samples from four freshwater and two marine sites of diverse ecological characteristics. The impact of the sample preservation and storage duration was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, diatom assemblage composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflected the site origin. Only rare taxa (< 100 reads) differed among preservation methods and storage durations. For biomonitoring purposes, freshwater ecological index values were not affected by the preservation method and storage duration tested (including ethanol preservation), all treatments returning the same ecological status for a site. This study contributes to consolidating diatom metabarcoding. Thus, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.

Characterisation and toxicological activity of three different Pseudo-nitzschia species from the northern Adriatic Sea (Croatia)

Diatoms of the genus Pseudo-nitzschia are cosmopolitans spread in seas and oceans worldwide, with more than 50 described species, dozens of which have been confirmed to produce domoic acid (DA). Here, we characterized and investigated the toxicological activity of secondary metabolites excreted into the growth media of different Pseudo-nitzschia species sampled at various locations in the northern Adriatic Sea (Croatia) using human blood cells under in vitro conditions. The results revealed that three investigated species of the genus Pseudo-nitzschia were capable of producing DA indicating their toxic potential. Moreover, toxicological data suggested all three Pseudo-nitzschia species can excrete toxic secondary metabolites into the surrounding media in addition to the intracellular pools of DA, raising concerns regarding their toxicity and environmental impact. In addition, all three Pseudo-nitzchia species triggered oxidative stress, one of the mechanisms of action likely responsible for the DNA damage observed in human blood cells. In line with the above stated, our results are of great interest to environmental toxicologists, the public and policy makers, especially in light of today's climate change, which favours harmful algal blooms and the growth of DA producers with a presumed negative impact on the public health of coastal residents.

Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization

Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 18S-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data.

Seasonal variations in extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water

Seasonal changes of microbial abundance and associated extracellular enzymatic activity in marine snow and in seawater were studied in the northern Adriatic during a three-year period. Marine snow was present during the entire period of investigation, although in higher concentrations during summer than during winter. Microorganisms densely colonized marine snow and aggregate-associated enzymatic activity was substantially higher (up to 105 times) than in seawater. Alkaline phosphatase activity (APA) and aminopeptidase activity in marine snow showed seasonal variations with higher values in late spring-summer than in autumn-winter, probably in response to changes in the quantity and quality of organic matter. The highest cell-specific bacterial activity was found for phosphatase, followed by peptidase, and the lowest was for glucosidases. Differential hydrolysis of marine snow-derived organic matter points to the well-known phosphorus limitation of the northern Adriatic and indicates preferential utilization of phosphorus- and nitrogen-rich organic compounds by microbes, while hydrolysis of polysaccharides seemed to be less important. In oligotrophic conditions during summer, organic matter released from marine snow might represent a significant source of substrate for free-living bacteria in seawater. For the first time microorganisms producing APA in marine snow were identified, revealing that dense populations of bacteria expressed APA, while cyanobacteria did not. Cyanobacteria proliferating in marine snow could benefit from phosphorus release by bacteria and nanoflagellates.

Insights into the life strategy of the common marine diatom Chaetoceros peruvianus Brightwell

Chaetoceros peruvianus is a marine diatom species with circumglobal distribution. While frequently observed, it appears never to dominate the marine phytoplankton community hence it can be characterized as a rather opportunistic, generalistic species. Here we present ecological interpretations from a long-term data set on marine microphytoplankton in the northern Adriatic Sea, where the abundancies and relative contributions of C. peruvianus were observed along a set of steep ecological gradients. Limited supply of dissolved inorganic phosphate was identified as the driving ecological factor for this ecosystem. In parallel C. peruvianus was cultivated in monoclonal cultures and its morphological and physiological reaction to replete and phosphorus depleted medium was analysed. C. peruvianus reacted to phosphorus depletion by an increase in cell height and length as well as thickness and length of setae. This morphological reaction included an increase in cellular volume and calculated carbon content. Additionally, it represents the transition between two described morphological varieties, C. peruvianus and C. peruvianus var. robusta. C. peruvianus showed a significant induction of extracellular alkaline phosphatase activity if grown in phosphate depleted medium. Microscopical analysis demonstrated this activity to be located exclusively on the setae of the cells.

The Ecology of One Cosmopolitan, One Newly Introduced and One Occasionally Advected Species from the Genus Skeletonema in a Highly Structured Ecosystem, the Northern Adriatic

The diatom genus Skeletonema is globally distributed and often an important constituent of the phytoplankton community. In the marine phytoplankton of the northern Adriatic Sea, we found three species of the genus Skeletonema: Skeletonema menzelii, Skeletonema marinoi and Skeletonema grevillei. Making use of the steep ecological gradients that characterise the northern Adriatic, along which we could observe those species, we report here on the ecological circumstances under which those species thrive and how their respective populations are globally connected. This is the first detailed ecological study for the species S. grevillei. This study is also the first report for S. grevillei for the Adriatic Sea and Mediterranean together with additional electron microscopic details on fresh in situ samples for this species. S. marinoi appears to clearly prefer strong freshwater influence and high nutrient concentrations delivered by low salinity waters. It can outcompete other diatom species and dominate microphytoplankton blooms. S. grevillei on the other hand appears to thrive in high nutrient concentrations triggered by water column mixing. It also appears to prefer higher salinity waters and coastal embayments. Genetic analysis of S. grevillei demonstrated a peculiar dissimilarity with isolates from coastal waters off Yemen, India, Oman and China. However, a closely related sequence was isolated from coastal waters off Japan. These results indicate that S. grevillei is an introduced species, possibly transported by ballast waters. S. menzelii is a sporadic visitor in the northern Adriatic, advected from rather oligotrophic middle Adriatic waters and never dominates the phytoplankton community in the northern Adriatic.

Depth-Related Alkaloid Variation in Mediterranean Aplysina Sponges

Total amounts and patterns of bromoisoxazoline alkaloids of Aplysina sponges from Croatia (Mediterranean Sea) were analyzed along an underwater slope ranging from 1.8 to 38.5 m. Total amounts of alkaloids varied from sample to sample and showed no correlation with depth. In contrast, striking differences of alkaloid patterns were found between sponges from shallow sites (1.8 - 11.8 m) and those collected from deeper sites (11.8 - 38.5 m). Sponges from shallow depths consistently exhibited alkaloid patterns typical for Aplysina aerophoba with aerophobin-2 (2) and isofistularin-3 (3) as main constituents. Sponges from deeper sites (below 11.8 m) resembled Aplysina cavernicola with aerothionin (4) and aplysinamisin- 1 (1) as major compounds. The typical A. cavernicola pigment 3,4-dihydroxyquinoline- 2-carboxylic acid (6), however, could not be detected in A. aerophoba sponges but was replaced by the A. aerophoba pigment uranidine (5) which appeared to be present in all sponge samples analyzed. During transplantation experiments sponges from sites below 30 m featuring the A. cavernicola chemotype of bromoisoxazoline alkaloids were translocated to shallower habitats (10 m). The alkaloid patterns in transplanted sponges were found to be stable over a period of 12 months and unaffected by this change in depth. In a further experiment, clones of Aplysina sponges from shallow depths of 5 - 6 m resembling the A. aerophoba chemotype were either kept in situ under natural light conditions or artificially shaded by excluding photosynthetically active radiation (PAR). Neither 4 nor 1 were detected in artificially shaded sponges over an observation period of 12 months. In summary, two chemically distinct types of Aplysina sponges were discovered in this study that proved to be remarkably stable with regard to the bromoisoxazoline patterns and unaffected either by changing the light conditions or depth. It is not clear presently whether the Aplysina sponges collected from depths < 11.8 m represent a new chemotype of A. cavernicola lacking the pigment 6 or whether we have incidentally come across a so far undescribed species of the genus Aplysina.

Toxin-producing Ostreopsis cf. ovata are likely to bloom undetected along coastal areas

Mass appearances of the toxic dinoflagellate genus Ostreopsis are known to cause dangerous respiratory symptoms in humans exposed to aerosols. The outbreaks can appear in shallow marine waters of temperate regions around the globe. We followed a massive bloom event on a public beach on the northern Adriatic coast near Rovinj, Croatia. We identified the responsible species and the produced toxins as well as the dynamics of the event with respect to environmental conditions. Ostreopsis cf. ovata appeared in masses from September through October 2010 on a public beach near Rovinj, Croatia but stayed undetected by public health organizations. Respiratory symptoms were observed whenever humans were exposed to substrate samples containing large numbers of Ostreopsis cells. During the mass abundance of O. cf. ovata also exposure to the aerosols on the beach evoked respiratory symptoms in humans. Our measurements showed high cell abundances and high toxin contents with a stable relative contribution of putative Palytoxin and Ovatoxins a-e. Artificial beach structures proved to dramatically reduce settling of the observed Ostreopsis biofilm. Blooms like those reported herein have a high potential to happen undetected with a high potential of affecting the health of coastal human populations. Increased monitoring efforts are therefore required to understand the ecology and toxicology of those bloom events and reduce their negative impact on coastal populations.

Assessment of bacterial endosymbiont diversity in Otiorhynchus spp. (Coleoptera: Curculionidae) larvae using a multitag 454 pyrosequencing approach

Background

Weevils of the genus Otiorhynchus are regarded as devastating pests in a wide variety of horticultural crops worldwide. So far, little is known on the presence of endosymbionts in Otiorhynchus spp.. Investigation of endosymbiosis in this genus may help to understand the evolution of different reproductive strategies in these weevils (parthenogenesis or sexual reproduction), host-symbiont interactions, and may provide a future basis for novel pest management strategy development. Here, we used a multitag 454 pyrosequencing approach to assess the bacterial endosymbiont diversity in larvae of four economically important Otiorhynchus species.

Results

High-throughput tag-encoded FLX amplicon pyrosequencing of a bacterial 16S rDNA fragment was used to characterise bacterial communities associated with different Otiorhynchus spp. larvae. By sequencing a total of ~48,000 PCR amplicons, we identified 49 different operational taxonomic units (OTUs) as bacterial endosymbionts in the four studied Otiorhynchus species. More than 90% of all sequence reads belonged either to the genus Rickettsia or showed homology to the phylogenetic group of “Candidatus Blochmannia” and to endosymbionts of the lice Pedicinus obtusus and P. badii. By using specific primers for the genera Rickettsia and “Candidatus Blochmannia”, we identified a new phylogenetic clade of Rickettsia as well as “Candidatus Nardonella” endosymbionts in Otiorhynchus spp. which are closely related to “Candidatus Blochmannia” bacteria.

Conclusions

Here, we used multitag 454 pyrosequencing for assessment of insect endosymbiotic communities in weevils. As 454 pyrosequencing generates only quite short sequences, results of such studies can be regarded as a first step towards identifying respective endosymbiotic species in insects. In the second step of our study, we analysed sequences of specific gene regions for a more detailed phylogeny of selected endosymbiont genera. As a result we identified the presence of Rickettsia and “Candidatus Nardonella” endosymbionts in Otiorhynchus spp.. This knowledge is an important step in exploring bacteria-insect associations for potential use in insect pest control.

AFM imaging of extracellular polymer release by marine diatom Cylindrotheca closterium (Ehrenberg) Reiman & J.C. Lewin

Extracellular polysaccharide production by marine diatoms is a significant route by which photosynthetically produced organic carbon enters the trophic web and may influence the physical environment in the sea. This study highlights the capacity of atomic force microscopy (AFM) for investigating diatom extracellular polysaccharides with a subnanometer resolution. Here we address a ubiquitous marine diatom Cylindrotheca closterium, isolated from the northern Adriatic Sea, and its extracellular polymeric substance (EPS) at a single cell level. We applied a simple procedure for AFM imaging of diatom cells on mica under ambient conditions (in air) to achieve visualization of their EPS with molecular resolution. The EPS represents a web of polysaccharide fibrils with two types of cross-linking: fibrils association forming junction zones and fibril-globule interconnections with globules connecting two or more fibrils. The fibril heights were 0.4-2.6 nm while globules height was in the range of 3-12 nm. Polymer networks of native gel samples from the Northern Adriatic and the network formed by polysaccharides extracted from the C. closterium culture share the same features regarding the fibril heights, pore openings and the mode of fibril association, proving that the macroscopic gel phase in the Northern Adriatic can be formed directly by the self-assembly of diatom released polysaccharide fibrils.

"Candidatus Paraholospora nucleivisitans", an intracellular bacterium in Paramecium sexaurelia shuttles between the cytoplasm and the nucleus of its host

An intracellular bacterium was discovered in two isolates of Paramecium sexaurelia from an aquarium with tropical fish in Münster (Germany) and from a pond in the Wilhelma zoological-botanical garden, Stuttgart (Germany). The bacteria were regularly observed in the cytoplasm of the host, but on some occasions they were found in the macronucleus of the host cell. In these cases, only a few, if any, bacteria were observed remaining in the cytoplasm. The bacterium was not infectious to P. sexaurelia or other species of Paramecium and appeared to be an obligate intracellular bacterium, while bacteria-free host cells were completely viable. The fluorescence in situ hybridisation (FISH) and comparative 16SrDNA sequence analyses showed that the bacterium belonged to a new genus, and was most closely, yet quite distantly, related to Holospora obtusa. In spite of this relationship, the new bacteria differed from Holospora by at least two biological features. Whereas all Holospora species reside exclusively in the nuclei of various species of Paramecium and show a life cycle with a morphologically distinct infectious form, for the new bacterium no infectious form and no life cycle have been observed. For the new bacterium, the name Candidatus Paraholospora nucleivisitans is suggested. The host P. sexaurelia is usually known from tropical and subtropical areas and is not a species typically found in Germany and central Europe. Possibly, it had been taken to Germany with fish or plants from tropical or subtropical waters. Candidatus Paraholospora nucleivisitans may therefore be regarded as an intracellular neobacterium for Germany.

Oxygen dynamics and transport in the Mediterranean sponge Aplysina aerophoba

The Mediterranean sponge Aplysina aerophoba kept in aquaria or cultivation tanks can stop pumping for several hours or even days. To investigate changes in the chemical microenvironments, we measured oxygen profiles over the surface and into the tissue of pumping and non-pumping A. aerophoba specimens with Clark-type oxygen microelectrodes (tip diameters 18-30 μm). Total oxygen consumption rates of whole sponges were measured in closed chambers. These rates were used to back-calculate the oxygen distribution in a finite-element model. Combining direct measurements with calculations of diffusive flux and modeling revealed that the tissue of non-pumping sponges turns anoxic within 15 min, with the exception of a 1 mm surface layer where oxygen intrudes due to molecular diffusion over the sponge surface. Molecular diffusion is the only transport mechanism for oxygen into non-pumping sponges, which allows total oxygen consumption rates of 6-12 μmol cm^-3 sponge day^-1. Sponges of different sizes had similar diffusional uptake rates, which is explained by their similar surface/volume ratios. In pumping sponges, oxygen consumption rates were between 22 and 37 μmol cm^-3 sponge day^-1, and the entire tissue was oxygenated. Combining different approaches of direct oxygen measurement in living sponges with a dynamic model, we can show that tissue anoxia is a direct function of the pumping behavior. The sponge-microbe system of A. aerophoba thus has the possibility to switch actively between aerobic and anaerobic metabolism by stopping the water flow for more than 15 min. These periods of anoxia will greatly influence physiological variety and activity of the sponge microbes. Detailed knowledge about the varying chemical microenvironments in sponges will help to develop protocols to cultivate sponge-associated microbial lineages and improve our understanding of the sponge-microbe-system.

Quiescent gemmules of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759), contain remarkably high levels of Hsp70 stress protein and hsp70 stress gene mRNA

With the onset of changing environmental conditions in autumn, the freshwater sponge Spongilla lacustris (Linnaeus, 1759) produces resistant stages (gemmules) which are in the state of quiescence. Gemmules stored at 8 degrees C remained quiescent; however, germination occurred within 24 hr after the water temperature was increased to 22.5 degrees C. Sponges hatched through the micropyle and subsequently built new spicules and a new canal system. The molecular and biochemical mechanisms which enable the gemmules to survive long periods of adverse conditions are not known. For the first time we focused on the role of the stress protein Hsp70 and the expression of hsp70 mRNA in S. lacustris during the development of gemmules in the state of quiescence into growing sponges. The partial sequence of hsp70 seems to be a true hsp gene since transcription could be clearly enhanced by temperature elevation. The results showed a large pool of cellular Hsp70 and hsp70 mRNA in gemmules during the state of quiescence. Within hours after a temperature trigger, the Hsp70 level decreased slowly and reached approximately the level of an adult sponge. Hsp70 presumably allows gemmules to stabilize their proteins and membranes during dormancy from autumn to spring when water temperatures change.