Caratteristiche strutturali e diversità delle comunità microbiche in sistemi acquatici ad alta variabilità ambientale: analisi dei batteri planctonici e dei biofilm
Author(s)
Lupini, Giuliano
Date Issued
March 20, 2012
Type
Doctoral Thesis
Abstract
The studies, carried out within the Doctorate, aimed to investigate the structure and the
function of the microbial community in different aquatic environments subject to
anthropogenic impacts. The Thesis was focused on assessing the structure and diversity
of the bacterioplankton in coastal waters with different trophic status and of the
bacterial community in riverine microbial biofilms, along a gradient of increasing
pollution.
The first part of the thesis (Chapter 3.1) was part of a CNR project on the role of
bacteria in the carbon cycle in the Adriatic Sea. Bacterial abundance and diversity were
assessed by molecular techniques (16S rDNA cloning and sequencing, CARD-FISH),
while bacterial activity was estimated by immunofluorescence techniques (BrdU
incorporation). All samples were collected during two oceanographic cruises (March
and November 2009) along a coastal-offshore transect with increasing values of
nutrients concentration. The results showed high seasonality in the water chemicophysical
characteristics passing from an oligotrophic state in March to a mesotrophic
state in November. In March, the low P concentration and the high values of N/P ratio
(156.3) seemed to limit the bacterial growth. In November, the increasing P
concentration and the N/P ratio (7.6) closed to the optimal value for bacterial growth,
brought to a higher bacterial activity and abundance, with higher values in the coastal
sites. Bacterial community structure was also related to the chemical-physical
characteristics. The community was dominated by the Alpha-Proteobacteria, typical of
marine environment and favoured by the low concentrations of nutrients; Cytophaga-
Flavobacteria showed a decreasing abundance in the offshore samples directly related
to particle organic matter (POC) concentration. The presence of Actinobacteria, typical
of the freshwater environments, found in higher percentages in the coastal stations also
confirmed the importance of freshwater input along the Adriatic coast. 230 sequences
were analyzed for 4 clone-library from surface and deep samples. Clone library showed
that the Alpha-Proteobacteria were mainly represented by with the genus SAR11 while
Gamma-Proteobacteria by Alteromonadales and many sequences of Cytophaga-
Flavobacteria were affiliated with Flavobacteriales.
The second part of the thesis (Chapter 3.2) was focused on the microbial communities
associated to biofilm in riverine environments. The study, carried out in the context of
an Italy-Spain exchange project, was aimed to investigate the effect of water pollution
on bacterial communities in Llobregat River, Spain. Bacterial abundance was lower in
the site subject to a lower antrophic impact in comparison with the downstream sites
where the community showed higher abundance. In these sites a dominance of Alphaand
Beta-Proteobacteria was observed. To better understand how the bacterial
communities respond to the pollutant impacts, biofilms growth in less polluted sites
were exposed to water from downstream sites in a traslocation experiment. At the end
of the experiment, the traslocated biofilm quickly became similar to the biofilm in the
impacted sites. Our results showed that quantitative and qualitative assessment of the
bacterial community composition could become an useful indicator of the water quality
and an early warning system for environmental changes.
The last part of thesis (Chapter 3.3), was focused on the optimization of CARD-FISH
protocol in combination with Confocal Laser Scanning Microscopy for the inspection of
riverine intact biofilm attached to the original substrate for simultaneous identification
and spatial localization of cells. Bacterial community composition was assessed during
the biofilm development by using artificial substrates following the dynamics of
specific bacterial clusters. Overall, we demonstrated that bacterial successional changes
can be described by applying the CARD-FISH protocol to intact biofilms, which are
ultimately from rivers, thereby avoiding biofilm detachment or manipulations. Our
approach, in combination with an appropriate image analysis procedure, could
contribute to elucidate how specific bacterial clusters participate to the development of
the complex biofilm structures and the mechanisms that regulate community
composition dynamic and cell dispersion in aquatic environments.
Additional information
Dottorato di ricerca in Ecologia e gestione delle risorse biologiche
Subjects
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