The microbiota that spoil long-life micro-filtered milk generally includes species of the genus
Microbacterium
. The metabolic properties of this of microorganisms that could potentially modify the ...quality of micro-filtered milk are still unexplored when compared to better-known microorganisms, such as the spore-forming
Bacillus
and
Paenibacillus
spp., and Gram-negative contaminants, such as species of the genera
Pseudomonas
and
Acinetobacter
. In this preliminary study, two strains of
Microbacterium
(
M. lacticum
18H and
Microbacterium
sp. 2C) isolated from micro-filtered milk were characterized in depth, both phenotypically and genotypically, to better understand their role in long-term milk spoilage. The study highlights the ability of these strains to produce high cell numbers and low acidification in micro-filtered milk under storage and shelf-life conditions. Phenotypic analyses of the two
Microbacterium
sp. isolates revealed that both strains have low proteolytic and lipolytic activity. In addition, they have the ability to form biofilms. This study aims to be a preliminary investigation of milk-adapted strains of the
Microbacterium
genus, which are able to grow to high cellular levels and perform slight but not negligible acidification that could pose a potential risk to the final quality of micro-filtered milk. Furthermore,
M. lacticum
18H and
Microbacterium
sp. 2C were genotypically characterized in relation to the characteristics of interest in the milk environment. Some protein-encoding genes involved in lactose metabolism were found in the genomes, such as β-galactosidase, lactose permease, and L-lactate dehydrogenase. The phenotypically verified proteolytic ability was supported in the genomes by several genes that encode for proteases, peptidases, and peptide transferases.
The novel multi-million read generating sequencing technologies are very promising for resolving the immense soil 16S rRNA gene bacterial diversity. Yet they have a limited maximum sequence length ...screening ability, restricting studies in screening DNA stretches of single 16S rRNA gene hypervariable (V) regions. The aim of the present study was to assess the effects of properties of four consecutive V regions (V3-6) on commonly applied analytical methodologies in bacterial ecology studies. Using an in silico approach, the performance of each V region was compared with the complete 16S rRNA gene stretch. We assessed related properties of the soil derived bacterial sequence collection of the Ribosomal Database Project (RDP) database and concomitantly performed simulations based on published datasets. Results indicate that overall the most prominent V region for soil bacterial diversity studies was V3, even though it was outperformed in some of the tests. Despite its high performance during most tests, V4 was less conserved along flanking sites, thus reducing its ability for bacterial diversity coverage. V5 performed well in the non-redundant RDP database based analysis. However V5 did not resemble the full-length 16S rRNA gene sequence results as well as V3 and V4 did when the natural sequence frequency and occurrence approximation was considered in the virtual experiment. Although, the highly conserved flanking sequence regions of V6 provide the ability to amplify partial 16S rRNA gene sequences from very diverse owners, it was demonstrated that V6 was the least informative compared to the rest examined V regions. Our results indicate that environment specific database exploration and theoretical assessment of the experimental approach are strongly suggested in 16S rRNA gene based bacterial diversity studies.
•Investigation on microbiomes of Parmigiano Reggiano and Grana Padano biogas plants.•Methanosarcina abundance correlates with ammonium concentration.•Methanoculleus more present under thermophilic ...conditions.•Thermotogales correlates with hydraulic retention time.•Acetate levels seems to influence Methanosarcina and Methanosaeta distribution.
The objective of this study was to investigate the effect of different animal feedings operated in two distinct PDO (protected designation of origin) cheese production areas (Parmigiano Reggiano and Grana Padano) on the microbiome of six full-scale biogas plants, by means of Illumina sequencing and qPCR techniques. The effects of feedstock (cattle slurry manure, energy crops, agro-industrial by-products), temperature (mesophilic/thermophilic), and operating time were also examined, as were the relationships between the predominant bacterial and archaeal taxa and process parameters. The different feedstocks and temperatures strongly affected the microbiomes. A more biodiverse archaeal population was highlighted in Parmigiano Reggiano area plants, suggesting an influence of the different animal feedings. Methanosarcina and Methanosaeta showed an opposite distribution among anaerobic plants, with the former found to be related to ammonium concentration. The Methanoculleus genus was more abundant in the thermophilic digester whereas representation of the Thermotogales order correlated with hydraulic retention time.
In recent decades, wild boar Sus scrofa populations have increased both in number and distribution in Italy, thus enhancing problems of cohabitation with humans. Crop damage represents one of the ...main sources of conflict; understanding the spatiotemporal variation of damage events and which factors increase the risk of damage is crucial to the development of effective management strategies. The aims of this study were to determine the impact of wild boar on croplands in the Special Protection Area “Risaie della Lomellina” (western Po Plain, northern Italy) and to formulate a risk prediction model through a binary logistic regression analysis. Damage events almost exclusively involved maize, and were concentrated in spring and summer. Sporadic cases of damage concerned rice, soybean and sorghum fields. The risk of damage was higher in fields close to forests, far from main roads, urban areas and continuous hedgerows, and in areas with low human population densities.
Biogas plants are a widespread renewable energy technology. However, the use of digestate for agronomic purposes has often been a matter of concern. It is controversial whether biogas plants might ...harbor some pathogenic clostridial species, which represent a biological risk. Moreover, the inhabitance of
Clostridium
hard-cheese spoiling species in anaerobic digesters can be problematic for hard-cheese manufacturing industries, due to the issue of cheese blowing defects. This study investigated the effect of mesophilic anaerobic digestion processes on the
Clostridium
consortia distribution over time. Specifically, three lab-scale CSTRs treating agricultural biomass were characterized by considering both the whole microbial community and the cultivable clostridial spores. It is assessed an overall reduction of the
Clostridium
genus during the anaerobic digestion process. Moreover, it was evidenced a slight, but steady decrease of the cultivable clostridial spores, mainly represented by two pathogenic species, C
. perfringens
and
C. bifermentans
, and one hard-cheese spoiling species,
C. butyricum
. Thus, it is revealed an overall reduction of the clostridial population abundance after the mesophilic anaerobic digestion treatment of agricultural biomass.
The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen ...production. The resulting hydrogen can then be funneled to anaerobic digesters for biogas upgrading (biomethanation) purposes (power-to-methane) or to produce high value-added compounds such as short-chain fatty acids (power-to-chemicals). Genome-centric metagenomics and metatranscriptomic analyses were performed to better understand the metabolic dynamics associated with H
injection in two different configurations of anaerobic digesters treating acidic wastes, specifically cheese manufacturing byproducts. These approaches revealed the key-genes involved in methanation and carbon fixation pathways at species level.
The biogas upgrading process in the single-stage configuration increased the CH
content by 7%. The dominant methanogenic species responsible for the upregulation of the hydrogenotrophic pathway in this reactor was Methanothermobacter wolfeii UC0008. In the two-stage configuration, H
injection induced an upregulation of CO
fixation pathways producing short-chain fatty acids, mainly acetate and butyrate. In this configuration, the abundant species Anaerobaculum hydrogeniformans UC0046 and Defluviitoga tunisiensis UC0050 primarily upregulated genes related to electron transport chains, suggesting putative syntrophisms with hydrogen scavenger microbes. Interestingly, Tepidanaerobacter acetatoxydans UC0018 did not act as an acetate-oxidizer in either reactor configurations, and instead regulated pathways involved in acetate production and uptake. A putative syntrophic association between Coprothermobacter proteolyticus UC0011 and M. wolfeii UC0008 was proposed in the two-stage reactor. In order to support the transcriptomic findings regarding the hydrogen utilization routes, an advanced bioconversion model was adapted for the simulation of the single- and two-stage reactor setups.
This is the first study investigating biogas reactor metatranscriptome dynamics following hydrogen injection for biomethanation and carbon fixation to short-chain fatty acids purposes. The same microbes showed different patterns of metabolic regulation in the two reactor configurations. It was observed an effect of the specialized acidogenic reactor on the overall microbial consortium composition and activity in the two-stage digester. There were also suggested the main species responsible for methanation, short-chain fatty acids production, and electron transport chain mechanisms, in both reactor configurations.
The composition of the bacterial consortia of the smear Italian cheeses and their role on quality and safety is still poorly understood. The objective of this study was to identify and characterize ...the bacterial communities present on the surface of five traditional Italian cheeses, Casera Valtellina, Scimudin, Formaggio di Fossa, Gorgonzola and Taleggio. DGGE analysis performed using total DNA obtained from cheese surfaces enabled us to identify the dominant bacterial populations. Bands showing different intensity and identified as
Staphylococcus,
Micrococcus,
Psychrobacter,
Enterococcus and
Brevibacterium species were detected on the surface of cheeses. The cluster analysis showed that Gorgonzola, Taleggio and Formaggio di Fossa cheeses present high similarity in their surface bacterial composition while major differences in the DGGE profiles were observed in Scimudin and Casera. The molecular taxonomical identification among the Gram positive isolates, reveals the presence of the following bacterial genera:
Staphylococcus,
Micrococcus,
Macrococcus,
Enterococcus,
Lactobacillus,
Carnobacterium,
Leuconostoc,
Brevibacterium,
Corynebacterium,
Brochothrix,
Bacillus. The combination of culture dependent and independent techniques allowed us to obtain information about the bacterial species covering the surface of five different traditional Italian cheeses.
Glaciers are important ecosystems, hosting bacterial communities that are adapted to cold conditions and scarcity of available nutrients. Several works focused on the composition of bacterial ...communities in glaciers and on the long-range atmospheric deposition of pollutants in glaciers, but it is not clear yet if ski resorts can represent a source of point pollution in near-by glaciers, and if these pollutants can influence the residing bacterial communities.
To test these hypotheses, 12 samples were analyzed in Madaccio Glacier, in a 3200ma.s.l. from two areas, one undisturbed and one close to a summer ski resort that is active since the 1930s. Chemical analyses found concentrations up to 43ngL−1 for PCBs and up to 168μgL−1 for PAHs in the contaminated area: these values are significantly higher than the ones found in undisturbed glaciers because of long-range atmospheric deposition events, and can be explained as being related to the near-by ski resort activities. Isolation of strains on rich medium plates and PCR-DGGE analyses followed by sequencing of bands allowed the identification of a bacterial community with phylogenetic patterns close to other glacier environments, with Proteobacteria and Actinobacteria the mostly abundant phyla, with Acidobacteria, Firmicutes and Cyanobacteria also represented in the culture-independent analyses. A number of isolates were identified by molecular and biochemical methods as phylogenetic related to known xenobiotic-degrading strains: glaciers subjected to chemical contamination can be important reservoirs of bacterial strains with potential applications in bioremediation.
•We analyzed bacterial diversity and pollutants in a ski resort close to a glacier.•The ski resort is a source of PCB and PAH contaminants.•Bacterial species phylogenetically close to xenobiotic degraders were found.•Organic contamination in glaciers can select xenobiotic degraders adapted to cold.
Pseudomonas fluorescens is a psychrotrophic species associated with milk spoilage because of its lipolytic and proteolytic activities. Consequently, monitoring P. fluorescens or its antecedent ...activity in milk is critical to preventing quality defects of the product and minimizing food waste. Therefore, in this study, untargeted metabolomics and peptidomics were used to identify the changes in milk related to P. fluorescens activity by simulating the low-temperature conditions usually found in milk during the cold chain. Both unsupervised and supervised multivariate statistical approaches showed a clear effect caused by the P. fluorescens inoculation on milk samples. Our results showed that the levels of phosphatidylglycerophosphates and glycerophospholipids were directly related to the level of contamination. In addition, our metabolomic approach allowed us to detect lipid and protein degradation products that were directly correlated with the degradative metabolism of P. fluorescens. Peptidomics corroborated the proteolytic propensity of P. fluorescens-contaminated milk, but with lower sensitivity. The results obtained from this study provide insights into the alterations related to P. fluorescens 39 contamination, both pre and post heat treatment. This approach could represent a potential tool to retrospectively understand the actual quality of milk under cold chain storage conditions, either before or after heat treatments.
This work investigated the microbiological quality and chemical profiles of two different dairy creams obtained by centrifugation vs. natural creaming separation systems. To this aim, an untargeted ...metabolomics approach based on UHPLC-QTOF mass spectrometry was used in combination with multivariate statistical tools to find potential marker compounds of the two different types of two dairy creams. Thereafter, we evaluated the chemical, microbiological and sensorial changes of a ricotta cheese made with a 30% milk cream (i.e., made by combining dairy creams from centrifugation and natural creaming separation) during its shelf-life period (12 days). Overall, microbiological analysis revealed no significant differences between the two types of dairy creams. On the contrary, the trend observed in the growth of degradative bacteria in ricotta during shelf-life was significant. Metabolomics revealed that triacylglycerols and phospholipids showed significant strong down-accumulation trends when comparing samples from the centrifugation and natural creaming separation methods. Additionally, 2,3-Pentanedione was among the best discriminant compounds characterising the shelf-life period of ricotta cheese (VIP score = 1.02), mainly related to sensorial descriptors, such as buttery and cheesy. Multivariate statistics showed a clear impact of the shelf-life period on the ricotta cheese, revealing 139 potential marker compounds (mainly included in amino acids and lipids). Therefore, the approach used showed the potential of a combined metabolomic, microbiological and sensory approach to discriminate ricotta cheese during the shelf-life period.
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