Konstantinos Ar. Kormas

Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176)

Abstract The prokaryotic community inhabiting the deep subsurface sediments in the Forearc Basin of the Nankai Trough southeast of Japan (ODP Site 1176) was analyzed by 16S rDNA sequencing. Sediment samples from 1.15, 51.05, 98.50 and 193.96 m below sea floor (mbsf) harbored highly diverse bacterial communities. The most frequently retrieved clones included members of the Green non-sulfur bacteria whose closest relatives come from deep subsurface environments, a new epsilon-proteobacterial phylotype, and representatives of a cluster of closely related bacterial sequences from hydrocarbon- and methane-rich sediments around the world. Archaeal clones were limited to members of the genus Thermococcus, and were only obtained from the two deepest samples.

Multiple biomarkers of pollution effects in caged mussels on the Greek coastline.

A suite of biomarkers was measured in caged mussels at areas impacted by different anthropogenic activities along the Greek coastline to assess biological effects of environmental pollution. Mussels were caged at coastal sites in the vicinity of major cities, in areas influenced by major industries, agricultural practices and in islands away from known sources of pollution. Biomarkers indicative of neurotoxicity (acetylcholinesterase, AchE), oxidative stress (catalase, CAT), phase II biotransformation of xenobiotics (glutathione S-transferase, GST), metal exposure (metallothioneins, MTs) and protein synthesis (RNA:DNA ratio) were measured to assess effects of various types of pollutants. AchE activity proved to be the most responsive biomarker with decreased values at sites influenced by agricultural, urban and industrial activities. Decreased CAT and GST activities and increased MTs levels were recorded at a number of anthropogenic-impacted sites. RNA:DNA ratio showed a biphasic response as both high and low values were found at impacted sites. Principal component analysis clearly distinguished sites receiving pollution inputs from non-polluted sites. The combination of the selected biomarkers used in caged mussels resulted useful in the assessment of the effects of environmental pollution.

Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea)

We investigated 16S rRNA gene diversity at a high sediment depth resolution (every 5 cm, top 30 cm) in an active site of the Kazan mud volcano, East Mediterranean Sea. A total of 242 archaeal and 374 bacterial clones were analysed, which were attributed to 38 and 205 unique phylotypes, respectively (> or = 98% similarity). Most of the archaeal phylotypes were related to ANME-1, -2 and -3 members originating from habitats where anaerobic oxidation of methane (AOM) occurs, although they occurred in sediment layers with no apparent AOM (below the sulphate depletion depth). Proteobacteria were the most abundant and diverse bacterial group, with the Gammaproteobacteria dominating in most sediment layers and these were related to phylotypes involved in methane cycling. The Deltaproteobacteria included several of the sulphate-reducers related to AOM. The rest of the bacterial phylotypes belonged to 15 known phyla and three unaffiliated groups, with representatives from similar habitats. Diversity index H was in the range 0.56-1.73 and 1.47-3.82 for Archaea and Bacteria, respectively, revealing different depth patterns for the two groups. At 15 and 20 cm below the sea floor, the prokaryotic communities were highly similar, hosting AOM-specific Archaea and Bacteria. Our study revealed different dominant phyla in proximate sediment layers.

Biodegradation of crude oil by thermophilic bacteria isolated from a volcano island

One-hundred and fifty different thermophilic bacteria isolated from a volcanic island were screened for detection of an alkane hydroxylase gene using degenerated primers developed to amplify genes related to the Pseudomonas putida and Pseudomonas oleovorans alkane hydroxylases. Ten isolates carrying the alkJ gene were further characterized by 16s rDNA gene sequencing. Nine out of ten isolates were phylogenetically affiliated with Geobacillus species and one isolate with Bacillus species. These isolates were able to grow in liquid cultures with crude oil as the sole carbon source and were found to degrade long chain crude oil alkanes in a range between 46.64% and 87.68%. Results indicated that indigenous thermophilic hydrocarbon degraders of Bacillus and Geobacillus species are of special significance as they could be efficiently used for bioremediation of oil-polluted soil and composting processes.

Diversity and spatial distribution of Prokaryotic communities along a sediment vertical profile of a Deep-Sea Mud Volcano

We investigated the top 30-cm sediment prokaryotic community structure in 5-cm spatial resolution, at an active site of the Amsterdam mud volcano, East Mediterranean Sea, based on the 16S rRNA gene diversity. A total of 339 and 526 sequences were retrieved, corresponding to 25 and 213 unique (≥98% similarity) phylotypes of Archaea and Bacteria, respectively, in all depths. The Shannon–Wiener diversity index H was higher for Bacteria (1.92–4.03) than for Archaea (0.99–1.91) and varied differently between the two groups. Archaea were dominated by anaerobic methanotrophs ANME-1, -2 and -3 groups and were related to phylotypes involved in anaerobic oxidation of methane from similar habitats. The much more complex Bacteria community consisted of 20 phylogenetic groups at the phylum/candidate division level. Proteobacteria, in particular δ-Proteobacteria, was the dominant group. In most sediment layers, the dominant phylotypes of both the Archaea and Bacteria communities were found in neighbouring layers, suggesting some overlap in species richness. The similarity of certain prokaryotic communities was also depicted by using four different similarity indices. The direct comparison of the retrieved phylotypes with those from the Kazan mud volcano of the same field revealed that 40.0% of the Archaea and 16.9% of the Bacteria phylotypes are common between the two systems. The majority of these phylotypes are closely related to phylotypes originating from other mud volcanoes, implying a degree of endemicity in these systems.

Temporal shifts of the Norway lobster (Nephrops norvegicus) gut bacterial communities.

The aim of this study was to investigate the gut bacterial communities of Nephrops norvegicus individuals, using a suite of molecular tools consisting of automated ribosomal intergenic spacer analysis, 16S rRNA gene-internal transcribed spacer clone libraries and FISH. The animals were collected from Pagasitikos Gulf, Greece, during different months of the year. The diversity of the gut bacterial communities was found to mostly vary with sampling time, which could be related to temporal variations in food supply. The 16S rRNA gene diversity analysis showed dominance of specific phylotypes for each month studied. February, May, July, August and October samples were rich in sequences related to the gammaproteobacterial genera Pseudoalteromonas, Psychrobacter and Photobacterium. September and December samples were dominated by phylotypes affiliated with uncultured representatives of Mollicutes, which are generally associated with the intestinal tracts of various animals. The presence of Gammaproteobacteria and uncultured Mollicutes in August and September samples, respectively, was further confirmed by FISH. None of the morphometric parameters considered was related to the temporal pattern of dominant bacterial communities.

Active biomonitoring in Greek coastal waters: Application of the integrated biomarker response index in relation to contaminant levels in caged mussels

An integrated approach using biomarkers and contaminant levels in mussels Mytilus galloprovincialis L. was employed to assess chemical contamination in Greek coastal waters within the framework of the MYTIMED program. Biomarkers (metallothioneins, glutathione S-transferase, catalase, acetylcholinesterase and RNA:DNA ratio) have been previously described in mussels caged at 14 sites in coastal areas influenced by different types of anthropogenic activities. This study applied a biomarker index, the Integrated Biomarker Response (IBR) to summarize biomarker responses and relate stress levels to concentrations of organochlorine compounds (PCBs, DDTs), polycyclic aromatic hydrocarbons (PAHs), and metals (Cu, Ni, Fe, Zn) measured in the mussel tissues. The IBR index indicated environmental stress at sites near cities and industries and was overall related to organic contaminants, but also elevated metal concentrations at certain sites. Slightly increased IBR values at few sites away from known pollution sources were not accompanied with increased contaminant levels suggesting stress possibly caused by natural factors. Results confirmed the usefulness of integration of biological effects measurements and chemical analysis for the assessment of chemical contamination in coastal waters.

Plankton Microorganisms Coinciding with Two Consecutive Mass Fish Kills in a Newly Reconstructed Lake

Lake Karla, Greece, was dried up in 1962 and its refilling started in 2009. We examined the Cyanobacteria and unicellular eukaryotes found during two fish kill incidents, in March and April 2010, in order to detect possible causative agents. Both microscopic and molecular (16S/18S rRNA gene diversity) identification were applied. Potentially toxic Cyanobacteria included representatives of the Planktothrix and Anabaena groups. Known toxic eukaryotes or parasites related to fish kill events were Prymnesium parvum and Pfiesteria cf. piscicida, the latter being reported in an inland lake for the second time. Other potentially harmful microorganisms, for fish and other aquatic life, included representatives of Fungi, Mesomycetozoa, Alveolata, and Heterokontophyta (stramenopiles). In addition, Euglenophyta, Chlorophyta, and diatoms were represented by species indicative of hypertrophic conditions. The pioneers of L. Karlas plankton during the first months of its water refilling process included species that could cause the two observed fish kill events.

Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata).

We compared the gut prokaryotic communities in wild, organically‐, and conventionally reared sea bream (Sparus aurata) individuals. Gut microbial communities were identified using tag pyrosequencing of the 16S rRNA genes. There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. Most of the Bacteria belonged to the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The number of bacterial operational taxonomic units (OTUs) was reduced from the wild to the conventionally reared fish, implying a response of the gut microorganisms to the supplied food and possibly alterations in food assimilation. The dominant bacterial OTU in all examined fish was closely related to the genus Diaphorobacter. This is the first time that a member of the β‐Proteobacteria, which dominate in freshwaters, are so important in a marine fish gut. In total the majority of the few Archaea OTUs found, were related to methane metabolism. The inferred physiological roles of the dominant prokaryotes are related to the metabolism of carbohydrates and nitrogenous compounds. This study showed the responsive feature of the sea bream gut prokaryotic communities to their diets and also the differences of the conventional in comparison to the organic and wild sea bream gut microbiota.

Inter-annual variability of soft bottom macrofaunal communities in two Ionian Sea lagoons

Inter-annual variation in the composition of the soft bottom macrobenthic communities of two undisturbed lagoons, in Amvrakikos Gulf, Ionian Sea, Greece, was investigated over three consecutive summers. The environmental parameters that showed the greatest variability were organic carbon of the sediment and salinity. The species found were typical of lagoonal systems, the most common and abundant of which were Abra ovata, Mytilaster minimus and, in the most enclosed areas, larvae of chironomids. Multivariate analysis registered community changes, which were mostly caused by changes in species dominance. Structural community characteristics such as number of species, number of individuals and diversity did not show significant differences among years except in the stations with least water exchange with the sea.