Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments.

Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.

Bacterial diversity of polluted surface sediments in the northern Adriatic Sea.

Samples were collected from sea sediments at seven sites in the northern Adriatic Sea that included six sites next to industrial complexes and one from a tourist site (recreational beach). The samples were assayed for alkanes and polycyclic aromatic hydrocarbons. The composition of the hydrocarbon samples suggested that industrial pollution was present in most cases. A sample from one site was also grown aerobically under crude oil enrichment in order to evaluate the response of indigenous bacterial populations to crude oil exposure. Analysis of 16S rRNA gene sequences showed varying microbial biodiversity depending on the level of pollution--ranging from low (200 detected genera) to high (1000+ genera) biodiversity, with lowest biodiversity observed in polluted samples. This indicated that there was considerable biodiversity in all sediment samples but it was severely restricted after exposure to crude oil selection pressure. Phylogenetic analysis of putative alkB genes showed high evolutionary diversity of the enzymes in the samples and suggested great potential for bioremediation and bioprospecting. The first systematic analysis of bacterial communities from sediments of the northern Adriatic Sea is presented, and it will provide a baseline assessment that may serve as a reference point for ecosystem changes and hydrocarbon degrading potential--a potential that could soon gain importance due to plans for oil exploitation in the area.

Relationships between heterotrophic bacteria and cyanobacteria in the northern Adriatic in relation to the mucilage phenomenon.

High variability of heterotrophic bacterial (HB; 0.1.10(9)-6.10(9) cells L(-1)), nanoflagellates (HNF; 0.02.10(6)-2.4.10(6) cells L(-1)) and cyanobacterial (CB; 10(6)-700.10(6) cells L(-1)) abundances were observed during approximately monthly measurements at six stations along the transect Po Delta-Rovinj from March 1999 to August 2002. Substantially higher values were observed during the stratification period (June-September) in the surface layer of the western stations that were under more direct influence of Po River discharges. Changes of the HB abundance were significantly correlated with temperature in the entire water column and chlorophyll a (Chla) concentration in the surface layer. The nutrients did not look to have directly influenced the HB growth, except orthophosphate in the eastern, more oligotrophic part of transect, where probably HB efficiently competed with phytoplankton for this nutrient. Temperature was also important for CB growth that, however, appeared to occur more intensively in waters with low nutrient concentrations. Probably, in these conditions CB can still develop, while larger autotrophs are strongly nutrient limited. In the upper water column of reduced salinity (35-37), the contributions of CB carbon biomass to the total picoplankton biomass (CB+HB) were mostly larger than 30% (up to 80%) in years with mucilage events (1991, 2000-2002) than in other years. For example, in 1999 only a few values were higher than 30% (up to 50%). In abundant presence of mucilaginous aggregates (e.g. in June 2000 and late June 2002) the chlorophyll a ascribed to CB accounted for much larger portions of total measured Chla. From these results it was concluded that cyanobacteria during mucilage events may play a substantially increased role both as primary producers and prey within the microbial loop of the northern Adriatic.

Fatty acid profiling of microbial community during aging of mucilaginous aggregates in the northern Adriatic.

Aggregates differing in size and phytoplankton community composition were sampled in winter/spring 2001 and summer 1997 and 2002 (during mucilaginous event) in the northern Adriatic Sea. The fatty acid profiles (FAME) were determined in aggregates, bacterial population was grown from each aggregate and each bacterial isolate from aggregate's plated cultures. All aggregates irrespective of the season, aggregate size or phytoplankton community composition contained isolates from three distinct groups, with fatty acid profiles corresponding to alpha-Proteobacteria, gamma-Proteobacteria and Cytophaga-Flavobacter (CF) complex but in different relative proportions. Fatty acid profiles of the bacterial population grown from each aggregate revealed either the domination of one group (gamma, alpha or CF) or contribution of more groups (gamma and CF; alpha and CF). Specifically, as the aggregates age a shift in favor of bacteria belonging to CF-complex and corresponding decrease in bacteria similar to that of Proteobacteria occur. During the aggregate aging process and degradation of the mucous matrix, besides bacterial succession, the phytoplankton growth took place inside the aggregates. Such an aging pattern was confirmed through laboratory experiments with aggregates inhabited by the diatom Cylindrotheca closterium.