Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

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.

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Evaluation of different methods to prevent Penicillium nordicum growth on and ochratoxin A production in country-style sausages

Penicillium nordicum is the main ochratoxin A (OTA)-producing fungal species isolated from artisanal sausages of different areas of Italy and other European countries. P. nordicum grows on and produces OTA in the sausage casing, thereby posing a health risk to Italian consumers, who commonly eat both the meat and casing of artisanal sausages. Different methods have been proposed to eliminate OTA and P. nordicum on the casings, including brushing, brushing and washing, the use of fungal starter cultures (Penicillium nalgiovense) and gaseous ozone. The aim of this study was to compare these methods with regard to eliminating the risk of OTA contamination in sausages. Three concentrations of gaseous ozone were assessed, i.e. 0.5, 1.0 and 1.5 mg/l. Only 1.5 mg/l prevented P. nordicum growth and production of OTA in sausages without influencing the physicochemical parameters and the sensory characteristic of the products. Application of this gaseous ozone concentration was then compared to the other methods, i.e. brushing, brushing and washing, a one-step starter culture of P. nalgiovense (inoculation after casing) and a two-step starter culture (inoculation after both casing and drying). The results obtained showed that only the use of gaseous ozone and a two-step starter culture of P. nalgiovense achieved complete inhibition of P. nordicum growth and OTA production. However, sensory analysis of the treated sausages showed that the use of starter cultures was the best method.

Influence of specific fermentation conditions on natural microflora of pomace in "Grappa" production

As reported in the European Community regulation, grappa is a spirit beverage made in Italy from marc that has been steam distilled or distilled after the addition of water. Grape marc from red grapes has already undergone alcoholic fermentation with the must and can be distilled immediately. Grape marc from white grapes does not contain ethanol but contains sugars that are fermented by spontaneous anaerobic fermentation during a storage period. The characteristic aroma of grappa consists of a large number of volatile compounds, which arise from various sources, the most important of which is yeast. Very few studies have been undertaken to characterize the natural populations of yeast during the fermentation of grape marc. The goal of this study was to understand how different pHs, temperatures and yeast starter cultures affect the growth and dynamics of yeast species involved in pomace fermentation, which could be the basis for improving the final quality of grappa production. We found that a temperature of 15°C has the greatest effect on improving the quality of the product. Unfortunately, due to the solid state of the grape marc and the impossibility of its mixing, it appears that acidification and the addition of yeast starter cultures during the silage period are not effective.

Hydroxyapatite formation from cuttlefish bones: kinetics

Highly porous hydroxyapatite (Ca(10)(PO(4))(6)·(OH)(2), HA) was prepared through hydrothermal transformation of aragonitic cuttlefish bones (Sepia officinalis L. Adriatic Sea) in the temperature range from 140 to 220°C for 20 min to 48 h. The phase composition of converted hydroxyapatite was examined by quantitative X-ray diffraction (XRD) using Rietveld structure refinement and Fourier transform infrared spectroscopy (FTIR). Johnson-Mehl-Avrami (JMA) approach was used to follow the kinetics and mechanism of transformation. Diffusion controlled one dimensional growth of HA, predominantly along the a-axis, could be defined. FTIR spectroscopy determined B-type substitutions of CO(3) (2-) groups. The morphology and microstructure of converted HA was examined by scanning electron microscopy. The general architecture of cuttlefish bones was preserved after hydrothermal treatment and the cuttlefish bones retained its form with the same channel size (~80 × 300 μm). The formation of dandelion-like HA spheres with diameter from 3 to 8 μm were observed on the surface of lamellae, which further transformed into various radially oriented nanoplates and nanorods with an average diameter of about 200-300 nm and an average length of about 8-10 μm.

Preparation of highly porous hydroxyapatite from cuttlefish bone

Hydroxyapatite structures for tissue engineering applications have been produced by hydrothermal (HT) treatment of aragonite in the form of cuttlefish bone at 200 degrees C. Aragonite (CaCO(3)) monoliths were completely transformed into hydroxyapatite after 48 h of HT treatment. The substitution of CO(3) (2-) groups predominantly into the PO(4) (3-) sites of the Ca(10)(PO(4))(6)(OH)(2) structure was suggested by FT-IR spectroscopy and Rietveld structure refinement. The intensity of the nu(3)PO(4) (3-) bands increase, while the intensity of the nu(2)CO(3) (2-) bands decrease with the duration of HT treatment resulting in the formation of carbonate incorporating hydroxyapatite. The SEM micrographs have shown that the interconnected hollow structure with pillars connecting parallel lamellae in cuttlefish bone is maintained after conversion. Specific surface area (S (BET)) and total pore volume increased and mean pore size decreased by HT treatment.

Description of the microflora of sourdoughs by culture-dependent and culture-independent methods

Four types of sourdoughs (L, C, B, Q) from artisanal bakeries in Northern Italy were studied using culture-dependent and culture-independent methods. In all samples, the yeast numbers ranged from 160 to 10(7)cfu/g, and the numbers of lactic acid bacteria (LAB) ranged from 10(3) to 10(9)cfu/g. The isolated LAB were sequenced, and a similarity was noted between two samples (C, Q), both in terms of the species that were present and in terms of the percentage of isolates. In these two samples, Lactobacillus plantarum accounted for 73% and 89% of the bacteria, and Lactobacillus brevis represented 27% and 11%. In the third sample (B), however, the dominant LAB isolate was Lb. brevis (73%), while Lb. plantarum accounted for only 27%. The fourth sourdough (L) was completely different from the others. In this sample, the most prominent isolate was Weisella cibaria (56%), followed by Lb. plantarum (36%) and Pediococcus pentosaceus (8%). In three out of four samples (L, C and Q), all of the yeasts isolated were identified as Saccharomyces cerevisiae, yet only Candida humilis (90%) and Candida milleri (10%) were isolated in the fourth sample (B). The microbial ecology of the sourdoughs was also examined with direct methods. The results obtained by culture-independent methods and DGGE analysis underline a partial correspondence between the DNA and RNA analysis. These results demonstrate the importance of using a combined analytical approach to explore the microbial communities of sourdoughs.

Fermentative stress adaptation of hybrids within the Saccharomyces sensu stricto complex

Along the fermentation process yeasts are affected by a succession of stress conditions that affect their viability and fermentation efficiency. Among the stress conditions the most relevant are high sugar concentration and low pH in musts, temperature and, as fermentation progresses, ethanol accumulation. Nowadays, due to the demanding nature of modern winemaking practices and sophisticated wine markets, there is an ever-growing search for particular wine yeast strains possessing a wide range of optimized, improved or novel enological characteristics. Traditionally, the species S. cerevisiae and S. bayanus within the Saccharomyces sensu stricto species are considered some of the most important yeast species involved in fermentation processes. However, in the last years, hybrid strains between the species S. cerevisiae, S. bayanus and S. kudriavzevii have been described as yeasts conducting the alcoholic fermentations and some of them are commercially available. Our results indicate that yeasts in the Saccharomyces sensu stricto complex were not affected by low pH or high glucose content in the media; however temperature and ethanol concentration variables appreciably affected their growth. The strains pertaining to S. cerevisiae were able to tolerate high temperature stress, whereas strains within S. bayanus and S. kudriavzevii were better adapted to growth at lower temperatures. Regarding to alcohol tolerance, S. cerevisiae is tolerating alcohol better than S. bayanus or S. kudriavzevii. Surprisingly, the natural hybrids between these species have adapted to growth under ethanol and temperature stress by inheriting competitive traits from one or another parental species. These results open new perspectives in the construction of new hybrid strains with biotechnological interest, as the characteristics of the parents may result in interesting combinations in the hybrids.

Modeling material saturation effects in microholographic recording

Microholographic data storage system model is presented that includes non-linear and non-local behavior of the storage material for accurate simulation of the system and optimization of the writing process. For the description of the photopolymer material a diffusion based nonlocal material model is used. The diffusion equation is solved numerically and the modulation of the dielectric constant is calculated. Diffraction efficiency of simulated microholograms and measurements were compared, and they show good agreement.

Moulds isolated from Istrian dried ham at the pre-ripening and ripening level

The aim of this study is to define the mould strains growing on the surface during the pre-ripening and the ripening phases of Istrian ham, and their toxic potential. The mould microflora was predominantly represented by five genera, which were isolated on the ham surfaces of three different producers investigated. The identified species were similar in the both tested periods, demonstrating that the contamination came mainly from the air and the ripening chambers (seasoning rooms), rather than the raw meat. Eurotium spp., Aspergillus spp. and Penicillium spp. were the main strains isolated. The presence and growth of the different strains depended on the temperature of ripening and the relative humidity in the ripening chambers, since the hams were home made products and not matured in controlled conditions. The toxic potential of isolated strains was also investigated. None of the tested moulds can produce mycotoxins and for this reason the Istrian hams do not represent a health hazard.

Differential malic acid degradation by selected strains of Saccharomyces during alcoholic fermentation

To produce a high-quality wine, it is important to obtain a fine balance between the various chemical constituents, especially between the sugar and acid content. The latter is more difficult to achieve in wines that have high acidity due to excess malic acid, since wine yeast in general cannot effectively degrade malic acid during alcoholic fermentation. An indigenous Saccharomyces paradoxus strain RO88 was able to degrade 38% of the malic acid in Chardonnay must and produced a wine of good quality. In comparison, Schizosaccharomyces pombe strain F effectively removed 90% of the malic acid, but did not produce a good-quality wine. Although commercially promoted as a malic-acid-degrading wine yeast strain, only 18% of the malic acid was degraded by Saccharomyces cerevisiae Lalvin strain 71B. Preliminary studies on the transcriptional regulation of the malic enzyme gene from three Saccharomyces strains, i.e. S. paradoxus RO88, S. cerevisiae 71B and Saccharomyces bayanus EC1118, were undertaken to elucidate the differences in their ability to degrade malic acid. Expression of the malic enzyme gene from S. paradoxus RO88 and S. cerevisiae 71B increased towards the end of fermentation once glucose was depleted, whereas no increase in transcription was observed for S. bayanus EC1118 which was also unable to effectively degrade malic acid.

Holographic reflection gratings in azobenzene polymers

Writing and reading of reflection gratings in films of an azo side-group polymer are reported. The gratings were induced holographically by use of an argon-ion laser at 488 nm. The measured diffraction efficiency was in the range 2-10%. To estimate the scattering of the reflected light within the material, we further characterized the gratings by calculating a characteristic transmission. A distinct minimum for this transmission was observed, which was redshifted farther from the writing wavelength for gratings written in 50-microm polymer samples.

C19 and C21 5 beta/5 alpha metabolite ratios in subjects treated with the 5 alpha-reductase inhibitor finasteride: comparison of male pseudohermaphrodites with inherited 5 alpha-reductase deficiency

Male subjects administered the 5 alpha-reductase inhibitor finasteride were studied to determine its effect on C19 and C21 5 alpha-metabolism. Plasma testosterone (T) and 5 alpha-dihydrotestosterone (DHT) were measured and T/DHT ratios determined at doses of 0.2-80 mg. Urinary etiocholanolone (5 beta)/androsterone (5 alpha) ratios and 5 beta/5 alpha metabolite ratios of cortisol, 11 beta-hydroxyandrostenedione, and corticosterone were also measured. The steroid profile was compared to male pseudohermaphrodites with inherited 5 alpha-reductase deficiency who have a global defect in C19 and C21 5 alpha-metabolism. The mean plasma DHT levels were decreased at all doses, resulting in elevated T/DHT ratios. The mean urinary etiocholanolone/androsterone, 11 beta-hydroxyetiocholanolone/11 beta-hydroxyandrosterone, tetrahydrocortisol/allotetrahydrocortisol, and tetrahydrocorticosterone/allotetrahydrocorticosterone ratios were elevated compared to pretreatment levels and placebo control values. The mean ratios appeared to be dose dependent for plasma T/DHT, urinary etiocholanolone/androsterone tetrahydrocorticosterone/allotetrahydrocorticosterone ratios. The mean 11 beta-hydroxyetiocholanolone-hydroxyandrosterone ratio was maximally elevated at the lowest doses. The results indicate that finasteride has a broad steroid spectrum inhibiting C19 and C21 5 alpha-steroid metabolism and affecting hepatic and peripheral 5 alpha-metabolism. These results suggest that a single gene codes for a single 5 alpha-reductase enzyme with affinity for multiple steroid substrates. The steroid profile is strikingly similar to that of male pseudohermaphrodites with inherited 5 alpha-reductase deficiency.