Microbial Diversity of Bacteria Involved in Biomineralization Processes in Mine-Impacted Freshwaters.

In order to increase the knowledge about geo-bio interactions in extreme metal-polluted mine waters, we combined microbiological, mineralogical, and geochemical analyses to study the indigenous sulfate-reducing bacteria (SRB) involved in the heavy metal (HM) biomineralization processes occurring in Iglesiente and Arburese districts (SW Sardinia, Italy). Anaerobic cultures from sediments of two different mining-affected streams of this regional framework were enriched and analyzed by 16S rRNA next-generation sequencing (NGS) technique, showing sequences closely related to SRB classified in taxa typical of environments with high concentrations of metals (Desulfovibrionaceae, Desulfosporosinus). Nevertheless, the most abundant genera found in our samples did not belong to the traditional SRB groups (i.e., Rahnella, Acinetobacter). The bio-precipitation process mediated by these selected cultures was assessed by anaerobic batch tests performed with polluted river water showing a dramatic (more than 97%) Zn decrease. Scanning electron microscopy (SEM) analysis revealed the occurrence of Zn sulfide with tubular morphology, suggesting a bacteria-mediated bio-precipitation. The inocula represent two distinct communities of microorganisms, each adapted to peculiar environmental conditions. However, both the communities were able to use pollutants in their metabolism and tolerating HMs by detoxification mechanisms. The Zn precipitation mediated by the different enriched cultures suggests that SRB inocula selected in this study have great potentialities for the development of biotechnological techniques to reduce contaminant dispersion and for metal recovery.

Omics approaches on fresh-cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment.

BACKGROUND: Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. RESULTS: An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. CONCLUSION: The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry.

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease.

In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease.

Correction: Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline.

[This corrects the article DOI: 10.1371/journal.pone.0156807.].

Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline.

Chronic airway infection is a hallmark feature of cystic fibrosis (CF) disease. In the present study, sputum samples from CF patients were collected and characterized by 16S rRNA gene-targeted approach, to assess how lung microbiota composition changes following a severe decline in lung function. In particular, we compared the airway microbiota of two groups of patients with CF, i.e. patients with a substantial decline in their lung function (SD) and patients with a stable lung function (S). The two groups showed a different bacterial composition, with SD patients reporting a more heterogeneous community than the S ones. Pseudomonas was the dominant genus in both S and SD patients followed by Staphylococcus and Prevotella. Other than the classical CF pathogens and the most commonly identified non-classical genera in CF, we found the presence of the unusual anaerobic genus Sneathia. Moreover, the oligotyping analysis revealed the presence of other minor genera described in CF, highlighting the polymicrobial nature of CF infection. Finally, the analysis of correlation and anti-correlation networks showed the presence of antagonism and ecological independence between members of Pseudomonas genus and the rest of CF airways microbiota, with S patients showing a more interconnected community in S patients than in SD ones. This population structure suggests a higher resilience of S microbiota with respect to SD, which in turn may hinder the potential adverse impact of aggressive pathogens (e.g. Pseudomonas). In conclusion, our findings shed a new light on CF airway microbiota ecology, improving current knowledge about its composition and polymicrobial interactions in patients with CF.

Bacterial community and proteome analysis of fresh-cut lettuce as affected by packaging.

With the growing demand of fresh-cut vegetables, a variety of packaging films are produced specifically to improve safety and quality of the fresh vegetables over the storage period. The aim of our work was to evaluate the influence of different packaging films on the quality of fresh-cut lettuce analyzing changes in bacterial community composition and modifications at the proteome level, by means of culture-dependent/culture-independent methods and differential gel electrophoresis combined with mass spectrometry analysis. Total viable counts indicated the presence of a highly variable and complex microbial flora, around a mean value of 6.26 log10 CFU g(-1). Analysis of terminal-restriction fragment length polymorphism data indicated that bacterial communities changed with packaging films and time, showing differences in community composition and diversity indices between the commercially available package (F) and the new packages (A and C), in the first days after packaging. Also proteomic analysis revealed significant changes, involving proteins related to energy metabolism, photosynthesis, plant defense and oxidative stress processes, between F and A/C packages. In conclusion, microbiological and proteomic analysis have proved to be powerful tools to provide new insights into both the composition of leaf-associated bacterial communities and protein content of fresh-cut lettuce during the shelf-life storage process.

Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function.

Cystic fibrosis (CF) is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD). Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV1). Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs) no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV1 (normal/mild vs moderate vs severe) were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good candidates for the development of predictive biomarkers of substantial decline in lung function.

Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region.

Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity.

Dynamics of hydrogen-producing bacteria in a repeated batch fermentation process using lake sediment as inoculum.

In this study, we evaluated the effectiveness of lake sediment as inoculum for hydrogen production through dark fermentation in a repeated batch process. In addition, we investigated the effect of heat treatment, applied to enrich hydrogen-producing bacteria, on the bacterial composition and metabolism. Denaturing gradient gel electrophoresis and molecular cloning, both performed using the 16S rDNA gene as target gene, were used to monitor the structure of the bacterial community. Hydrogen production and bacterial metabolism were analysed via gas chromatography and high-performance liquid chromatography. Both treated and non-treated inocula were able to produce high amounts of hydrogen. However, statistical analysis showed a clear difference in their bacterial composition and metabolism. The heat treatment favoured the growth of different Clostridia sp., in particular of Clostridium bifermentans, allowing the production of a constant amount of hydrogen over prolonged time. These cultures showed both butyrate and ethanol fermentation types. Absence of heat treatment allowed species belonging to the genera Bacillus, Sporolactobacillus and Massilia to outgrow Clostridia sp. with a reduction in hydrogen production and a significant metabolic change. Our data indicate that lake sediment harbours bacteria that can efficiently produce hydrogen over prolonged fermentation time. Moreover, we could show that the heat treatment stabilizes the bacterial community composition and the hydrogen production.

Vertical distribution of bacterioplankton in Lake Averno in relation to water chemistry.

The effects of environmental factors on bacterioplankton distribution along the water column of Lake Averno (Naples, Italy) have been investigated by means of denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments, and multivariate analysis applied to molecular data and physico-chemical parameters. Bacterial richness, estimated from DGGE profiles, remains constant throughout the water column, whereas archaeal richness increases with depth. Moreover, archaeal richness was significantly correlated to most of the measured abiotic variables, whereas bacterial richness did not. Analysis of sequences from DGGE bands revealed that the dominant bacterial populations belong to Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Bacteroidetes and Firmicutes, whereas sequences of the archaeal DGGE bands are affiliated to Methanomicrobiales and Methanosarcinales orders. Moreover, bacterial sequences affiliated to Proteobacteria and Bacteroidetes do not group closely to typical freshwater lineages/clades/tribes within these phyla. Bacterioplankton distribution along the water column was apparently correlated with the vertical gradient of physico-chemical parameters as a statistically significant relationship between most of them with grouping of specific taxonomic units was observed.

Sustainable power production in a membrane-less and mediator-less synthetic wastewater microbial fuel cell.

Microbial fuel cells (MFCs) fed with wastewater are currently considered a feasible strategy for production of renewable electricity. A membrane-less MFC with biological cathode was built from a compact wastewater treatment reactor and fed with synthetic wastewater. When operated with an external resistance of 250 Omega, the MFC produced a long-term power of about 70 mW/m(2) for 10 months. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the cathode biomass when the MFC was closed on a 2100 Omega external resistance showed that the sequenced bands were affiliated with Firmicutes, alpha-Proteobacteria,beta-Proteobacteria, gamma-Proteobacteria, and Bacteroidetes groups. When the external resistance was varied between 250 and 2100 Omega, minimum sustainable resistance decreased from 900 to 750 Omega, while maximum sustainable power output decreased from 32 to 28 mW/m(2). It is likely that these effects were caused by changes in the microbial ecology of anodic and cathodic biomass attached to the electrodes. Results suggest that cathodic biomass enrichment in "electroactive" bacteria may improve MFCs power output in a similar fashion to what has been already observed for anodic biomass.