Responsible: Raffaella Casotti

Activities

The laboratory of Microbial Ecology carries on research on marine microorganisms (mainly diatoms and autotrophic/heterotrophic picoplankton) studying their diversity, activity and metabolic functions as well as their interactions with the environment, both physical-chemical and biological. The activities are held mainly by direct methods, that is, independent from cultivation, but monospecific cultures are also used to test specific hypotheses or further characterize microorganisms. The fields of activity cover the biological oceanography, ecophysiology and marine ecology in general.
The laboratory also implements the technical and instrumental approaches for the study of microorganisms, mainly as regards the use of flow cytometry for the monitoring of marine plankton and for the development of early warning systems for biological environmental risk.

Experimental systems

• Thermostated cabinets for growing microalgae and bacteria under controlled light and temperature conditions.
• Tanks for experiments on board ships or outdoors for incubations and manipulations of natural plankton communities.

Analysis

• Counts and measurements of optical parameters (scatter and fluorescence) on cells and unicellular organisms by flow cytometry and epifluorescence microscopy.
• Estimates of growth rates and grazing of picoplankton.
• In situ hybridization with oligonucleotide probes for the characterization of bacterial communities.
• Estimates of DNA content of algae and cell lines by flow cytometry (including dynamics of the cell cycle).
• DNA and RNA extraction for metagenomics and metatranscriptomics.
• Analysis of cellular concentrations of picophytoplankton with scanning flow cytometers at high frequency in both laboratory and on board boats.
• Analysis of concentrations and cellular properties of marine bacteria with prototype automatic coloring module.

Instrumentation

• Conventional flow cytometry.
• Scanning flow cytometer with automated sampling module.
• Laminar flow hood.
• Thermostated cabinets for algal and bacterial cultures.
• Epifluorescence microscope with camera.
• Basic instrumentation for laboratory (centrifuges, thermostated baths, pHmeter, filtration rigs, sonicators, refrigerators and freezers).

Coordinator: Gabriele Procaccini

Scientific activities

Strumentazione di base per la biologia molecolare (PCR, centrifughe, apparati elettroforetici, transilluminatore, bagni termostatici, spettrofotometro, fluorimetro, pH-metro, bilancia di precisione)
Gene gun (apparecchio per la trasformazione biolistica)
In the laboratory of Molecular Ecology and Functional Genomics we carry out studies addressing ecological questions, using molecular approaches. The laboratory covers research  activities ranging from molecular phylogeny and taxonomy to phylogeography and population genetics, using sequence analysis and analysis of polymorphic markers, such as microsatellites and SNPs. It also deals with the study of gene function through functional genomics approaches and reverse genetics (mainly production of transgenic lines of diatoms). We also makes use of analysis of environmental genomics and comparative transcriptomics, and we carry out gene expression studies in natural and controlled conditions (RNA-Seq, RT-qPCR).

Experimental systems

• Mesocosms for maintaining benthic organisms under controlled conditions.
• Walk-in chamber for microalgal cultures.

Analysis

• DNA extraction, purification and quantification.
• RNA extraction, purification, quantification and reverse transcription.
• Protein extraction and quantification.
• Sample preparation for RT-qPCR in plates.
• Samples preparation for massive sequencing.
• Samples preparation for sequence analysis.
• Samples preparation for fragments analysis.
• single and multiplex PCR.
• Electrophoresis on agarose and acrylamide gel.
• Statistical analysis of population genetics and molecular phylogeny.
• Primers design, analysis of electropherograms.
• Cloning and bacterial transformation.
• Preparation of plasmid DNA (mini and maxi prep).
• Biolistic transformation and cultivation of GM crops.
• Algal cultures.
• Colorimetric assays with fluorescent vital dyes and microscopic analysis.
• Southern blot, Northern blot.
• Western blot and enzyme assays (colorimetric, ELISA).
• Use of specialized software for the analysis of protein and nucleotide databases and for the exploration of genomes.

Equipments

• Basic equipment for molecular biology (PCR, centrifuges, electrophoresis apparatus, transilluminator, thermostatic baths, spectrophotometer, fluorometer, pH meter, balance).
• Gene gun (apparatus for biolistic transformation).
• Hoods for algal cultures.
• Microscopes.
• Mixer Mill (Tissue Lyser).
• PC and software for molecular analysis.
• Fume hood.
• TurboGen (equipment for generating marine turbulence).

Reference: Filomena Ristoratore

Laboratory equipped for the study of molecular aspects of physiological responses of marine organisms at various stages of life cycle.
Includes areas equipped for electrophysiology and molecular biology, cell culture and basic laboratory equipments.

Systems for experimentation

• Genomic amplification and gene expression.
• Electrophysiology.

Analysis

• Physiological responses of marine organisms to stimuli.
• Membrane potential during fertilization events of marine organisms.
• Electrophysiology and Neurophysiology.
• Physiological analysis of immune responses in marine invertebrates.

Equipments

• Eletrophysiological Set-ups.
• Cell culture apparata.
• Molecular biology (nucleic acids and proteins).

Reference: Remo Sanges

Laboratory equipped for studies of computational genomics throughout bioinformatics approaches.

Systems for experimentation

Databases, high throughput functional genomics.

Analysis

Computational approaches, bioinformatics, comparative genomics, data-mining (genomics and transcriptomics in marine organisms).

Strumentazioni

• Personal computers.
• Workstations and servers.