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Aims: One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community’s viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses. Methods and results: We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties. Conclusions: The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil. [ABSTRACT FROM AUTHOR]

Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil. [ABSTRACT FROM AUTHOR]

In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops. [ABSTRACT FROM AUTHOR]

Abstract A 14th Century illuminated codex underwent an extensive restoration in 1739. The intervention was necessary because the volume was “rotten”. Some purple stains are still visible and passed through multiple pages in the thickness of the volume, with a pattern that suggested a resurgence of the infection after the restoration of the manuscript. The unusual appearance of the halos and the light-pink colouring of some of the spots indicated that a topical treatment of some kind could have been carried out. The stains were analysed by non-invasive and micro-invasive methods in order to reveal the chemicals used to disinfect or bleach them and the structural effects of the treatment on the collagen fibres. The chemical compound used to treat the stains of the codex contained sulphur and potassium, it was strongly acidic and in a liquid form. Based on both the results and the knowledge of that time, we hypothesised that in 1739 the restorer was aware of “infectious” nature of the stains and tried to stop the action of microorganisms. The attempt to stop the process would be the testimony of a diffuse knowledge on biodeterioration phenomena, not yet consolidated, but already present. Graphical abstract Image 1 Highlights • 14th Century codex restored in 1739 because “rotten” by a microbial attack. • Microbial purple stains were reactivated after the restoration. • Structural and chemical evidence that a chemical compound was used on the stains. • Restorers aware of “infectious” nature of the stains: tried to stop them. • Hypothesis: tacit knowledge on biodeterioration phenomena since the 18th Century. [ABSTRACT FROM AUTHOR]

The gelatin-silver halide black and white prints represent an enormous photography heritage with a great value. Unaesthetic phenomena, the foxing stains that are caused by microbial growth on surface, have been described in stamps, drawings, books, and tissues but, until now, scarcely for photographic materials. In this study, a combination of various techniques, including culture-dependent and culture-independent approaches (RNA and DNA analysis), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) and μ-Raman spectroscopy supported by X-ray fluorescence analysis (XRF), permitted to describe the microbial contamination dynamics of foxing stains present on the surface of two gelatin-silver halide photographs. The investigation provided also information on the effects of microbial activity on the materials' chemistry of the two prints. The action of microbial community resulted locally in either (a) formation of mixed aluminum-iron-potassium phosphate compounds that could be attributed to the hydrolytic activity of bacteria, (b) leaching of barite, (c) precipitation of a mixture of oxides, and (d) a change in the barium sulfate chemical structures. [ABSTRACT FROM AUTHOR]

Abstract: Archives and libraries all over the world suffer from biodeterioration of writings caused by microorganisms, especially fungi. With traditionally used culture-dependent methods, only a small amount of effectively colonising organisms is detected. Restoration and maintenance of written cultural heritage is therefore problematic due to incomplete knowledge of the deterioration agents. In the present study, culture-independent molecular methods were applied to identify fungal communities colonising paper samples of different composition and age. Nucleic-acid-based strategies targeting the internally transcribed spacer (ITS) regions, which are nested in the nuclear rDNA repeats, were selected to investigate the fungal diversity on paper. The ITS regions possess a high variation among taxonomically distinct fungal species and even within the species. With this aim, several molecular biological methods were optimised for working with paper materials. Here, we introduce a DNA extraction protocol, which allowed the direct extraction of PCR-amplifiable DNA from samples derived from different kinds of paper. The DNA extracts were used to amplify either the ITS1 or ITS2 region by using different fungi-specific primer sets. The ITS-amplified regions were subsequently analysed by denaturing gradient gel electrophoresis (DGGE). Conditions for DGGE analysis, gradient, voltage, and running time, were established to accurately discriminate different fungal species in complex communities. Pure fungal strains were used to constitute a marker for further comparative investigations of historic papers. [Copyright &y& Elsevier]

We, a group of concerned researchers and conservators, are very grateful to the 17th International Biodeterioration and Biodegradation Symposium (IBBS17) organizing committee and to the International Biodeterioration and Biodegradation Society president Brenda Little for giving us this opportunity to have a Panel Discussion on the “Past, Present and Future” of biodeterioration studies during the IBBS17 on September 6–8, 2017 in Manchester, U.K. A total of twenty-three of us, including a number of young scientists, joined the discussion and a few colleagues gave their inputs by mail in advance. It is our pleasure to summarize all information collected from the one-hour discussion in Manchester and to share them openly for future research planning and for establishment of a common ground to build new initiatives. [ABSTRACT FROM AUTHOR]