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© 2012 Wertheim, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Beyond the Gene List: Exploring Transcriptomics Data in Search for Gene Function, Trait Mechanisms and Genetic Architecture

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.

Ostreopsis spp. are benthic dinoflagellates that are known to cause harmful algae blooms. They are known producers of a range of palytoxins and ovatoxins. During bloom events those toxins can be found in high concentrations in benthic biofilms, in the water column as well as in coastal aerosols. Ostreopsis spp. distribution and related harmful algae blooms are well documented along the western Adriatic coast and parts of the western Mediterranean. Little was known so far about its distribution along the eastern Adriatic coast which presents very different ecological conditions with respect to the western Adriatic coast. A high resolution sampling regime along the eastern coast of the northern Adriatic revealed a dense population structure and high abundances along that coast line. Samples from the middle and southern Adriatic confirmed the presence of Ostreopsis ovata along the entire eastern Adriatic coast. Our results demonstrate, that oligotrophic rocky shores can be a very suitable habitat for O. ovata. Massive bloom events with record abundances and toxin concentrations are reported. The population along the north- eastern Adriatic coast share one ITS1-5.8S-ITS2 genotype with most of the populations recorded around the Mediterranean.

The marine diatom genusLeptocylindrusis a major component of phytoplankton blooms in coastal ecosystems worldwide, however, little is known about the ecology and meticulous species composition of this genus in the Adriatic Sea. Although Leptocylindrus danicus andL. minimus have been reported from numerous studies conducted in Adriatic, there has been neither unequivocal species identification nor focused examination of the temporal abundance of Leptocylindrus in this region. In a recent reappraisal of Leptocylindrus by Nanjappa et al. (2013) five species and one new genus were identified using both morphological and molecular markers. We here describe the temporal distribution of the genus Leptocylindrus based on 45 years of records, revealing that this diatom is a key component of the seasonal phytoplankton cycle, with greatest abundance in the spring and autumn. Using light and scanning electron microscopy as well as genetic analysis based on the nuclear- encoded rDNA regions, our study unambiguously revealed three species new for the Adriatic Sea, Leptocylindrus hargravesii, Leptocylindrus convexus and Leptocylindrus aporus. Furthermore, we investigated the growth, auxospore and resting spore formation of one of the Leptocylindrus species under different nutrient regimes. The ecology, physiology and evolution of this significant diatom genus should be further investigated.

Besides being a highly sensitive ecosystem, the Adriatic Sea is also an important seaway for international and local shipping, which poses a serious risk on the transfer of harmful aquatic organisms and pathogens (HAOP) by ships. Monitoring programs and surveillance activities would be of limited efficacy if carried out on a local scale only. The first step in setting up a common Adriatic approach towards unwanted threats to the environment from the transfer of HAOP was to prepare an inventory of organisms in ports. Phytoplankton diversity was determined through the port baseline survey in twelve Adriatic ports in years 2011, 2014 and 2015. Phytoplanktonic HAOP were identified as species, either native or non-indigenous (NIS) that can trigger harmful algal blooms (HAB). A list of 689 taxa was prepared and among them 52 were classified as HAB and five as NIS. Records of toxigenic NIS (Pseudo-nitzschia multistriata, Ostreopsis species including O. cf. ovata) indicate that the intrusion of non-native invasive phytoplankton species has already occurred in some Adriatic ports. The seasonal occurrence and abundance of HAOP offers a solid baseline for a monitoring design in ports in order to prevent possible expansion of HAOP outside their native region.

The northern Adriatic is a suitable ecosystem for observing phytoplankton under a variety of different ecological conditions. This shallow basin is characterized by a multitude of steep and quickly changing gradients (e.g. nutrients), both temporal and spatial. The current systems and the major freshwater input (River Po) generate strong gradients in utrient concentrations with an expressed N/P imbalance and sustained phosphate limitation. The genus Chatoceros is among the most diverse and pecies rich diatoms often dominating the phytoplankton community in the Adriatic Sea. There is a big number of species belonging to this genus with different physiology, seasonality and ecology. We analyzed species from the genus Chaetoceros, with a special focus on their metabolic eaction towards phosphate limitation. Here we report data on species-specific growth rates under different nutrient regimes, phosphate uptake rates, alkaline phosphatase activity, localization and activation patterns and characteristics of alkaline phosphatase activity. Our results demonstrate a high interspecific variation in metabolic responses to phosphate limitation in sympatric congeneric species. Ecological characteristics and hence significance and function appears hence to be defined on the species level and appears far from homogeneous within genera. This results in a highly structured planktonic ecosystem that allows for a high level of sympatric congeneric species diversity.

Ovalbumin (OVA)-sensitized BALB/c mice were i.n. instilled with recombinant TNF-related apoptosis inducing ligand (TRAIL) 24 hours before OVA challenge. The total number of leukocytes and the levels of the chemokine CXCL-1/KC significantly increased in the bronchoalveolar lavage (BAL) fluids of allergic animals with respect to control littermates, but not in the BAL of mice i.n. pretreated with recombinant TRAIL before OVA challenge. In particular, TRAIL pretreatment significantly reduced the BAL percentage of both eosinophils and neutrophils. On the other hand, when TRAIL was administrated simultaneously to OVA challenge its effect on BAL infiltration was attenuated. Overall, the results show that the i.n. pretreatment with TRAIL down-modulated allergic airway inflammation.