Genotyping-by-sequencing provides new genetic and taxonomic insights in the critical group of Centaurea tenorei.

Centaurea L. is one of the most widespread, differentiated, and critical genera of Asteraceae in the Euro-Mediterranean area, with more than 100 currently recognized species inhabiting the region. The controversial C. tenorei group, narrowly endemic to the Peninsula of Sorrento (Campania region, southern Italy), includes three weakly differentiated microspecies: C. tenorei Guss. ex Lacaita, C. montaltensis (Fiori) Peruzzi and C. lacaitae Peruzzi. However, their taxonomic distinctiveness and relationships with close or sympatric species are still unclear. In particular, the existence in several localities of individuals with intermediate morphology suggests inadequate taxonomic assessment within the group or hybridization and introgression with other species. In this study we aimed at defining population structure in this complex. With this objective, we sampled the three currently accepted species from their loci classici (i.e., the localities in which the taxa were originally described) and from other localities throughout the range, including populations of difficult identification occurring where the ranges of different taxa overlap. We employed a panel of SNPs obtained via genotyping-by-sequencing for investigations on genetic structure, admixture and ploidy inference, the latter also compared with chromosome counts. Our results showed that Centaurea tenorei s.l. is consistently tetraploid, contradicting the current taxonomy that was also based on ploidy level. Population structure analyses indicated the presence of four to seven clusters, most of which with clear evidence of admixture. Furthermore, contrarily to what previously supposed, we demonstrated a remarkable contribution of C. deusta, more that of C. cineraria in the genetic make-up of C. tenorei. However, we found a population of C. cineraria outside its ecological range, probably driven by climate change, which could be responsible in the future of further hybridization phenomena.

Characterisation of Environmental Biofilms Colonising Wall Paintings of the Fornelle Cave in the Archaeological Site of Cales.

Caves present unique habitats for the development of microbial communities due to their peculiar environmental conditions. In caves decorated with frescoes, the characterization of microbial biofilm is important to better preserve and safeguard such artworks. This study aims to investigate the microbial communities present in the Fornelle Cave (Calvi Risorta, Caserta, Italy) and their correlation with environmental parameters. The cave walls and the wall paintings have been altered by environmental conditions and microbial activity. We first used light microscopy and scanning electron microscopy (SEM) and X-ray diffraction to characterise the biofilm structure and the mineral composition of substrata, respectively. Then, using both culture-dependent (Sanger sequencing) and culture-independent (automated ribosomal intergenic spacer analysis, ARISA) molecular methods, we demonstrated that the taxonomic composition of biofilms was different across the three substrata analysed and, in some cases, positively correlated with some environmental parameters. We identified 47 taxa in the biofilm samples, specifically 8 bacterial, 18 cyanobacterial, 14 algal and 7 fungal taxa. Fungi showed the highest number of ARISA types on the tuff rock, while autotrophic organisms (cyanobacteria and algae) on the frescoes exposed to light. This study confirms that caves constitute a biodiversity-rich environment for microbial taxa and that, in the presence of wall paintings, taxonomic characterization is particularly important for conservation and restoration purposes.

UV-C Irradiation as a Tool to Reduce Biofilm Growth on Pompeii Wall Paintings.

This study focuses on the experimentation of a method based on the use of UV-C irradiation to eliminate the biofilms present in a tomb located in the necropolis of Porta Nocera, in Pompeii. For this study, the autotrophic component of the biofilm was isolated in the laboratory, while, contemporarily, the characterization of the composition of the pigments of the frescoes took place on original fragments, which had already detached from the tomb and were examined in situ. These preliminary analyses were necessary for the recreation of test samples in the laboratory, which closely matched the original surfaces. Artificial biofilms were used for experimental exposure to UV-C radiation. The exposure to UV-C radiation was carried out at different distances for a fixed time interval. The effectiveness of the biocidal action was assessed by employing optical microscopy techniques, through a careful visual assessment of the area occupied by the biofilm on the different test samples, using a photographic survey, as well as by means of colorimetric measurements using spectrometric techniques. In order to obtain an additional parameter to evaluate the death rate of microorganism cultures exposed to the UV-C radiation, the concentrations of the photosynthetic pigments were also measured by spectrophotometry. Results showed that biofilms were completely eradicated by radiation, and no change in pigment color was observed.

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths.

In this work, we want to investigate the impact of different substrates and different environmental condition on the biofilm communities growing on plaster, marble, and mortar substrates inside the Herculaneum Suburban Baths. To do so, we measured environmental conditions and sampled biofilm communities along the walls of the baths and used culture-dependent and -independent molecular techniques (DGGE) to identify the species at each sampling sites. We used the species pool to infer structure and richness of communities within each site in each substrate, and confocal light scanning microscopy to assess the three-dimensional structure of the sampled biofilms. To gather further insights, we built a meta-community network and used its local realizations to analyze co-occurrence patterns of species. We found that light is a limiting factor in the baths environment, that moving along sites equals moving along an irradiation gradient, and that such gradient shapes the community structure, de facto separating a dark community, rich in Bacteria, Fungi and cyanobacteria, from two dim communities, rich in Chlorophyta. Almost all sites are dominated by photoautotrophs, with Fungi and Bacteria relegated to the role of rare species., and structural properties of biofilms are not consistent within the same substrate. We conclude that the Herculaneum suburban baths are an environment-shaped community, where one dark community (plaster) and one dim community (mortar) provides species to a "midway" community (marble).

Use of high-strength electromagnetic radiation to remove phototrophic biofilms from terracotta artifacts.

A novel technique, effective in eliminating biodeteriogens from biofilms encrusting terracotta artifacts, is presented here. This method is based on the use of high-strength electromagnetic radiation (EMR) in the radiofrequency band. Shards of terracotta from historical pots at the Botanical Garden of Naples, Italy, were used. The shards, after sterilization, were inoculated with several phototrophic microorganisms previously isolated from whole terracotta pots. The newly formed biofilms were exposed to EMR amplitude modulated by a train of rectangular pulses with Tr = 200 ns repetition time and 10% duty cycle. The exposure protocol consisted of three applications of 2 h each, every other day. Denaturing gradient gel electrophoresis analyses conducted on the newly formed biofilms showed that, after the first exposure to EMR, all species in the biofilms but one were still alive. The second exposure resulted in the disappearance of 9 out of 13 species that were initially present on the samples. After the third exposure, all species disappeared. Superficial layers of terracotta from the exposed samples, transferred to a culture medium at 24 °C for 72 h, did not show any re-growing of organisms. Petrographic analyses of the sampleswere carried out before and after the treatments; they showed that exposure to EMR did not cause structural alterations in the treated substrates. Moreover, the amplitude of the EMR that samples were exposed to was not high enough to cause any significant increase in the temperature of the substrates; that is, no thermal effect, which is the most relevant effect when matter or organisms containing water are exposed to EMR, was observed. Finally, the field strength of the EMR showed to be non-invasive for the artifacts and non-dangerous for operators and the environment as compared to other techniques adopted in the field of conservation of cultural heritage.

Cryptic dispersal of Cyanidiophytina (Rhodophyta) in non-acidic environments from Turkey.

Cyanidiophytina are a group of polyextremophilic red algae with a worldwide, but discontinuous colonization. They are restricted to widely dispersed hot springs, geothermal habitats, and also some human-altered environments. Cyanidiophytina are predominant where pH is prohibitive for the majority of eukaryotes (pH 0.5-3). Turkey is characterized by areas rich in volcanic activity separated by non-volcanic areas. Here we show that Cyanidiophycean populations are present in thermal baths located around Turkey on neutral/alkaline soils. All known genera and species within Cyanidiophytina were detected in Turkey, including Galdieria phlegrea, recorded up to now only in Italian Phlegrean Fields. By phylogenetic analyses, Turkish G. sulphuraria strains are monophyletic with Italian and Icelandic strains, and with Russian G. daedala strains. G. maxima from Turkey clustered with Icelandic, Kamchatka, and Japanese populations. The discovery of Cyanidiophytina in non-acidic Turkish soils raises new questions about the ecological boundaries of these extremophilic algae. This aids in the understanding of the dispersal abilities and distribution patterns of this ecologically and evolutionarily interesting group of algae.

Comparative assessment of the quality of commercial black and green tea using microbiology analyses.

BACKGROUND: Drinking tea constitutes a tradition which is deeply rooted in the culture of several countries. Moreover, in recent years, tea consumption is growing all over the world. Improper herbal tea storage (long periods, humid environments) represents a relevant health hazard for consumers because of the growth of bacteria and molds. RESULTS: This study analyzed 32 samples of commercially available black and green teas - purchased from southern Italy markets and online-shops - and the monitoring of microbiological quality of the tea bag content was performed. Evaluations were conducted with the aim of characterizing pathogens indicated by the European and American guidelines (total bacterial count, fungi and Escherichia coli) and on the research of Pseudomonas spp. and Clostridium perfringens. The presence of ochratoxin A in tea matrix-leaves and infusions was further assessed, using a validated and accredited HPLC-FLD method. Microbial loads, for over 80% samples, ranged from 1.0 × 102 to 2.8 × 105 CFU/g tea: most of identified microorganisms were classified as Bacillaceae. The utilization of rapid detection and identification methods (PCR and sequencing), allowed the characterization of strains of Pseudomonas psychrotolerans, Staphylococcus warneri, Pantoea gaviniae and the isolation of one strain of Clostridium perfringens, whose ability to produce toxins can result in harmful outcomes for consumers. Fungi were isolated from 70% samples: the most prevalent molds were Aspergillus niger strains, followed by Aspergillus tubingensis. Ochratoxin A was detected in 22 of 32 tea solid samples investigated: concentrations resulted over the indicated limits for food products for 50% samples. CONCLUSIONS: Results obtained demonstrated the need to develop targeted regulations for the safety of herbal teas.

Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity.

Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.

Biofilms in churches built in grottoes.

We investigated microorganisms dwelling on rocks, walls and paintings in two votive chapels built in grottoes in the Region of Campania, Italy. One grotto was near the coast in an area with a Mediterranean climate, and the other grotto was inland on a mountain in an area with a cold continental climate. Color and distribution of biofilms in various areas of the grottoes were examined. Microbial components of biofilms were identified by light and electron microscopy and by molecular techniques (DNA analyses and Automatic rRNA Intergenic Spacer Analysis). Biofilms were also analyzed by X-ray diffraction to detect inorganic constituents deriving from rocks in the grottoes and walls of the churches and by X-ray fluorescence to detect the elements that made up the pigments of the mural paintings; optical cross sections were used to observe their relationships with substrata. Species of eubacteria, cyanobacteria and green algae were identified. Some of these species occurred in both grottoes, while others were exclusive to only one of the grottoes. The diversity of species, their common or exclusive occurrence in the grottoes, the relationships among microbial communities and the differences in color and distribution of biofilms were discussed on the basis of the different climatic factors affecting the two grottoes and the different inorganic components of substrata.

Genetic structure of a novel biofuel-producing microorganism community.

Biofuels are an important alternative, renewable source of energy in the face of the ongoing depletion of fossil fuels. Cheese whey is a dairy industry waste characterized by high lactose concentration, which represents a significant environmental problem. Bio-ethanol production by cheese whey could be an effective nonvegetable source for renewable energy production. Here, we report the isolation of a mixed microbial population, able to produce ethanol as main fermentation product from fermenting whey. The microbial consortium has been used to perform a batch fermentation of crude whey in both anoxic and hypoxic conditions. Maximum ethanol concentrations achieved in this study was obtained using the mixed culture in hypoxic conditions, grown at pH 4 and 30 °C, with ethanol production yield of 60 g/L. Our research has pointed out an alternative way to both dispose and valorize cheese whey, a dairy by-product that could cause water pollution and harm to the environment if not properly treated.

Chlamydomonas pitschmannii Ettl, a little known species from thermoacidic environments.

Three Chlamydomonas strains were isolated from the soils of a hot spring located in the Campi Flegrei Caldera (Naples, Italy). Ecophysiological, morpho-cytological and molecular features were used to characterize these isolates and to compare them with chlamydomonax acidophila strains from algal culture collections. The strains were collected from three points of the volcanic site, differing in their physico-chemical conditions. Among the examined Chlamydomonas strains, only the isolates from Campi Flegrei could grow optimally at pH values < or =3.0. These isolates also showed a high tolerance to desiccation and high temperatures, not evidenced by the other Chlamydomonas strains included in the study. 18S rDNA phylogeny indicates that the isolates from Campi Flegrei are closely related to Chlamydomonas pitschmannii and two strains isolated in Canada and Europe, that have been designated as Chlamydomonas acidophila. A Chlamydomonas acidophila strain isolated from the type locality in Japan is less closely related according to its molecular phylogeny, and can also be discerned by light and electron microscopy. Moreover, vegetative cells and sporangia of Chlamydomonas acidophila from Japan showed a median trilaminar structure not observed in the other strains. Our results show that Chlamydomonas pitschmannii could represent a hitherto unknown extremophilic Chlamydomonas species.

Mitochondrial cytochrome b DNA sequence variations: an approach to fish species identification in processed fish products.

The identification of fish species in food products is problematic because morphological features of the fish are partially or completely lost during processing. It is important to determine fish origin because of the increasing international seafood trade and because European Community Regulation 104/2000 requires that the products be labeled correctly. Sequence analysis of PCR products from a conserved region of the cytochrome b gene was used to identity fish species belonging to the families Gadidae and Merluccidae in 18 different processed fish products. This method allowed the identification of fish species in all samples. Fish in all of the examined products belonged to these two families, with the exception of one sample of smoked baccalà (salt cod), which was not included in the Gadidae cluster.

Phylogenetic relationships and taxonomic position of Chlorella-like isolates from low pH environments (pH < 3.0).

BACKGROUND: Little is known about phytoplankton communities inhabiting low pH environments such as volcanic and geothermal sites or acidic waters. Only specialised organisms are able to tolerate such extreme conditions. There is, thus, low species diversity. We have characterised the previously isolated acid tolerant Chlorella-like microalgae Viridiella fridericiana and Chlorella protothecoides var. acidicola by microscopical and biomolecular methods in order to assess their phylogenetic relationships. RESULTS: Both isolates belong to the trebouxiophycean lineage of chlorophytes. 18S and ITS1 sequence data clearly confirm that Viridiella fridericiana constitutes a new genus apart from the morphologically similar and likewise acid tolerant microalga Chlorella saccharophila. Chlorella protothecoides var. acidicola on the other hand is not a variety of Chlorella protothecoides but falls within a heterogeneous cluster consisting of Nannochloris, "Chlorella" spec. Yanaqocha, and Koliella, and is most closely related to algae which were also isolated from extreme environments. CONCLUSIONS: The distribution of acid tolerant strains in the 18S rRNA tree shows that acquisition of acid tolerance was unlikely a monophyletic event in green microalgae. We propose that different strains have independently adapted to extreme environments. Some of them have spread worldwide and were able to colonise other extreme habitats. Considering the problems of successfully isolating acid tolerant strains, acidic soils could represent an unsuspected source of biological diversity with high potential for biotechnological utilisations.