Changes in Soil Microbial Communities Induced by Biodegradable and Polyethylene Mulch Residues Under Three Different Temperatures.

Mulching is a common method increasing crop yield and achieving out-of-season production; nevertheless, their removal poses a significant environmental danger. In this scenario, the use of biodegradable plastic mulches comes up as a solution to increase the sustainability of this practice, as they can be tilled in soil without risk for the environment. In this context, it is important to study the microbial response to this practice, considering their direct involvement in plastic biodegradation. This study evaluated the biodegradation of three commercial mulch residues: one conventional non-biodegradable mulch versus two biodegradable ones (white and black compostable Mater-Bi mulches). The experiment was conducted under three incubation temperatures (room temperature 20-25 °C, 30 °C, and 45 °C) for a 6-month trial using fallow agricultural soil. Soil without plastic mulch residues was used as a control. White mater-bi biodegradable mulch residues showed higher degradation rates up to 88.90% at 30 °C, and up to 69.15% at room temperature. Furthermore, incubation at 45 °C determines the absence of degradation for all types of mulch considered. Moreover, bacterial alpha diversity was primarily influenced by plastic type and temperature, while fungal populations were mainly affected by temperature. Beta diversity was impacted by all experimental variables. Predicted functional genes crucial for degrading complex substrates, including those encoding hydrolases, cutinases, cellobiosidases, and lipases, were derived from 16S rRNA gene sequencing data. Cluster analysis based on predicted enzyme-encoding gene abundance revealed two clusters, mainly linked to sampling time. Finally, core microbiome analysis identified dominant bacterial and fungal taxa in various soil-plastic ecosystems during degradation, pinpointing species potentially involved in plastic breakdown. The present study allows an assessment of how different temperatures affect the degradation of mulch residues in soil, providing important insights for different climatic growing zones. It also fills a gap in the literature by directly comparing the effects of biodegradable and polyethylene mulches on soil microbial communities.

Water retting process with hemp pre-treatment: effect on the enzymatic activities and microbial populations dynamic.

Proper retting process of hemp stems, in which efficient separation of cellulose fiber from the rest of the stem is promoted by indigenous microorganisms able to degrade pectin, is essential for fiber production and quality. This research aimed to investigate the effect of a pre-treatment dew retting in field of hemp stalks on the pectinolytic enzymatic activity and microbiota dynamic during lab-scale water retting process. A strong increase in the pectinase activity as well as in the aerobic and anaerobic pectinolytic concentration was observed from 14 to 21 days, especially using hemp stalks that were not subjected to a pre-retting treatment on field (WRF0 0.690 ± 0.05 U/mL). Results revealed that the microbial diversity significantly varied over time during the water retting and the development of microbiota characterizing the water retting of hemp stalks of different biosystems used in this study was affected by pre-treatment conditions in the field and water retting process and by an interaction between the two methods. Although at the beginning of the experiment a high biodiversity was recorded in all biosystems, the water retting led to a selection of microbial populations in function of the time of pre-treatment in field, especially in bacterial populations. The use of hemp stems did not subject to a field pre-treatment seems to help the development of a homogeneous and specific pectinolytic microbiota with a higher enzymatic activity in respect to samples exposed to uncontrolled environmental conditions for 10, 20, or 30 days before the water retting process. KEY POINTS: • Microbial diversity significantly varied over time during water retting. • Water retting microbiota was affected by dew pre-treatment in the field. • Retting of no pretreated hemp allows the development of specific microbiota with high enzymatic activity.

A novel bio-solid phase extractor for preconcentrations of Hg and Sn in food samples.

An ecofriendly preconcentration method was developed based on the use of Geobacillus galactosidasius sp. nov immobilized on Amberlite XAD-4 as an adsorbent for the preconcentrations of Hg and Sn. SEM-EDX performed for the investigation of surface functionality and morphology. The detailed investigations of factors such as pH of the solution, flow rate, interfering ions and sample volume have been thanks to the optimization of the pre-concentration system. The optimum pHs were found as 5.0-7.0 for Hg and Sn and also the optimum flow rates were determined as 2 mL min-1 for recovery of Hg and Sn. Under the best experimental conditions, limits of detections (LOD) were found as 0.53 ng mL-1 for Hg and 0.27 ng mL-1 for Sn. RSDs were calculated as 8.2% for Hg and 6.9% for Sn. The process was validated to use certified references (fish samples). ICP-OES was used to measure the levels of Hg and Sn in various real meal patterns after the devised technique was used. Concentrations of Hg and Sn were quantitively measured on gluten-free biscuit, flour, rice, Tuna fish, meat, chicken meat, potato, chocolate, coffee, tap water, energy drink and mineral water samples with low RSD. The developed method emerges as an innovative technology that will eliminate the low cost and toxic effect.

Graphene-Based and Surface-Enhanced Raman Spectroscopy for Monitoring the Physio-Chemical Response of Thermophilic Bacterial Spores to Low Temperatures Exposure.

Monitoring the spore life cycle is one of the main issues in several fields including environmental control, sustainable ecosystems, food security, and healthcare systems. In this framework, the study of the living organism resistance to extreme conditions like those mimicking space environments is particularly interesting. The assessment of the local change of the pH level can be extremely useful for this purpose. An optical physiometer method based on the Raman response of the graphene, which is able to locally sense pH of a fluid on a micrometric scale, has been recently proposed. Due to the presence of π -bonds at the surface, the electronic doping of graphene is determined by the external conditions and can be electrochemically controlled or altered by the contact with an acid or alkaline fluid. The doping level affects the vibrational energies of the graphene that can be monitored by conventional Raman spectroscopy. In addition, Surface-Enhanced Raman Spectroscopy (SERS) can give direct information on the biochemical changes occurring in spore components. In this work, we propose the joint use of Graphene-Based Raman Spectroscopy (GbRS) and SERS for the monitoring of the response of spores to exposure to low temperatures down to 100 K. The spores of the thermophilic bacterium Parageobacillus thermantarcticus isolated from an active volcano of Antarctica (Mt. Melbourne) were investigated. These spores are particularly resistant to several stressing stimuli and able to adapt to extreme conditions like low temperatures, UV irradiation, and γ -rays exposure. The results obtained showed that the joint use of GbRS and SERS represents a valuable tool for monitoring the physio-chemical response of bacterial spores upon exposure to stressing stimuli.

Resistance and Raman spectroscopy analysis of Parageobacillus thermantarcticus spores after γ-ray exposure.

Spores of the genus Bacillus are able to resist ionizing radiations and therefore they are a suitable biological model for studies in Astrobiology, i.e. the multidisciplinary approach to the study of the origin and evolution of life on Earth and in the universe. The resistance to γ-radiation is an important issue in Astrobiology in relation to the search for bacterial species that could adapt to life in space. This study investigates the resistance of spores of the thermophilic bacteria Parageobacillus thermantarcticus to γ-rays. The analysis of spores' response to irradiation at a molecular level is performed by means of Raman spectroscopy that allows to get insights in the sequence of events taking place during inactivation. The role of the γ-rays' dose in the inactivation of spores is also investigated, allowing to highlight the mechanism(s) of inactivation including DNA damage, protein denaturation and calcium dipicolinate levels.

Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy.

Strain Corallo1T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, ß-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1T. A draft genome sequence of strain Corallo1T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1T are C16:1, n-C16:0 and C18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1T (= DSM 27495T = CIP 110630T).

Survival and Adaptation of the Thermophilic Species Geobacillus thermantarcticus in Simulated Spatial Conditions.

Astrobiology studies the origin and evolution of life on Earth and in the universe. According to the panspermia theory, life on Earth could have emerged from bacterial species transported by meteorites, that were able to adapt and proliferate on our planet. Therefore, the study of extremophiles, i.e. bacterial species able to live in extreme terrestrial environments, can be relevant to Astrobiology studies. In this work we described the ability of the thermophilic species Geobacillus thermantarcticus to survive after exposition to simulated spatial conditions including temperature's variation, desiccation, X-rays and UVC irradiation. The response to the exposition to the space conditions was assessed at a molecular level by studying the changes in the morphology, the lipid and protein patterns, the nucleic acids. G. thermantarcticus survived to the exposition to all the stressing conditions examined, since it was able to restart cellular growth in comparable levels to control experiments carried out in the optimal growth conditions. Survival was elicited by changing proteins and lipids distribution, and by protecting the DNA's integrity.

The effect of bacterial and archaeal populations on anaerobic process fed with mozzarella cheese whey and buttermilk.

Dairy wastes can be conveniently processed and valorized in a biorefinery value chain since they are abundant, zero-cost and all year round available. For a comprehensive knowledge of the microbial species involved in producing biofuels and valuable intermediates from dairy wastes, the changes in bacterial and archaeal population were evaluated when H2, CH4 and chemical intermediates were produced. Batch anaerobic tests were conducted with a mixture of mozzarella cheese whey and buttermilk as organic substrate, inoculated with 1% and 3% w/v industrial animal manure pellets. The archaeal methanogens concentration increased in the test inoculated at 3% (w/v) when H2 and CH4 production occurred, being 1 log higher than that achieved in the test inoculated at 1% (w/v). Many archaeal species, mostly involved in the production of CH4, were identified by sequencing denaturing gradient gel electrophoresis (DGGE) bands. Methanoculleus, Methanocorpusculum and Methanobrevibacter genera were dominant archaea involved in the anaerobic process for bioenergy production from mozzarella cheese whey and buttermilk mixture.

Aeribacillus composti sp. nov., a thermophilic bacillus isolated from olive mill pomace compost.

A Gram-stain-positive, aerobic, endospore-forming, thermophilic bacterium, strain N.8T, was isolated from the curing step of an olive mill pomace compost sample, collected at the Composting Experimental Centre (CESCO, Salerno, Italy). Strain N.8T, based on 16S rRNA gene sequence similarities, was most closely related to Aeribacillus pallidus strain H12T (=DSM 3670T) (99.8 % similarity value) with a 25 % DNA-DNA relatedness value. Cells were rod-shaped, non-motile and grew optimally at 60 °C and pH 9.0, forming cream colonies. Strain N.8 was able to grow on medium containing up to 9.0 % (w/v) NaCl with an optimum at 6.0 % (w/v) NaCl. The cellular membrane contained MK-7, and C16 : 0 (48.4 %), iso-C17 : 0 (19.4 %) and anteiso-C17 : 0 (14.6 %) were the major cellular fatty acids. The DNA G+C content was 40.5 mol%. Based on phenotypic characteristics, 16S rRNA gene sequences, DNA-DNA hybridization values and chemotaxonomic characteristics, strain N.8T represents a novel species of the genus Aeribacillus, for which the name Aeribacillus composti sp. nov. is proposed. The type strain is N.8T (=KCTC 33824T=JCM 31580T).

Structural characterization of the lipid A from the LPS of the haloalkaliphilic bacterium Halomonas pantelleriensis.

Halomonas pantelleriensis DSM9661(Τ) is a Gram-negative haloalkaliphilic bacterium isolated from the sand of the volcanic Venus mirror lake, closed to seashore in the Pantelleria Island in the south of Italy. It is able to optimally grow in media containing 3-15 % (w/v) total salt and at pH between 9 and 10. To survive in these harsh conditions, the bacterium has developed several strategies that probably concern the bacteria outer membrane, a barrier regulating the exchange with the environment. In such a context, the lipopolysaccharides (LPSs), which are among the major constituent of the Gram-negative outer membrane, are thought to contribute to the restrictive membrane permeability properties. The structure of the lipid A family derived from the LPS of Halomonas pantelleriensis DSM 9661(T) is reported herein. The lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different numbers of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of ESI FT-ICR mass spectrometry and chemical analysis. Preliminary immunological assays were performed, and a comparison with the lipid A structure of the phylogenetic proximal Halomonas magadiensis is also reported.

Strong Notch activation hinders bevacizumab efficacy in advanced colorectal cancer.

AIM: To assess the role of Notch activation in predicting bevacizumab efficacy in colorectal cancer (CRC). MATERIALS & METHODS: Notch activation was evaluated by immunohistochemistry (IHC) on 65 CRC enrolled within randomized clinical trials assessing first-line bevacizumab-based chemotherapy and on 21 CRC treated with chemotherapy alone. RESULTS: Strong Notch (IHC 3+) activation was negatively associated with response (18 vs 62% in low Notch cases [IHC 0, 1, 2+]; p = 0.016), progression-free survival (4.9 vs 12.1 months; p = 0.002) and overall survival (19.3 vs 30.4 months; p = 0.039). No correlation was found between Notch activation and clinical outcome in CRC treated with chemotherapy alone. CONCLUSION: A potential role of Notch activation in the antitumor activity of bevacizumab could be hypothesized.

Alginate hydrogels coated with chitosan for wound dressing.

In this work, a coating of chitosan onto alginate hydrogels was realized using the water-soluble hydrochloride form of chitosan (CH-Cl), with the dual purpose of imparting antibacterial activity and delaying the release of hydrophilic molecules from the alginate matrix. Alginate hydrogels with different calcium contents were prepared by the internal setting method and coated by immersion in a CH-Cl solution. Structural analysis by cryo-scanning electron microscopy was carried out to highlight morphological alterations due to the coating layer. Tests in vitro with human mesenchymal stromal cells (MSC) were assessed to check the absence of toxicity of CH-Cl. Swelling, stability in physiological solution and release characteristics using rhodamine B as the hydrophilic model drug were compared to those of relative uncoated hydrogels. Finally, antibacterial activity against Escherichia coli was tested. Results show that alginate hydrogels coated with chitosan hydrochloride described here can be proposed as a novel medicated dressing by associating intrinsic antimicrobial activity with improved sustained release characteristics.

The Lipid A from the haloalkaliphilic bacterium Salinivibrio sharmensis strain BAG(T).

Lipid A is a major constituent of the lipopolysaccharides (or endotoxins), which are complex amphiphilic macromolecules anchored in the outer membrane of Gram-negative bacteria. The glycolipid lipid A is known to possess the minimal chemical structure for LPSs endotoxic activity, able to cause septic shock. Lipid A isolated from extremophiles is interesting, since very few cases of pathogenic bacteria have been found among these microorganisms. In some cases their lipid A has shown to have an antagonist activity, i.e., it is able to interact with the immune system of the host without triggering a proinflammatory response by blocking binding of substances that could elicit such a response. However, the relationship between the structure and the activity of these molecules is far from being completely clear. A deeper knowledge of the lipid A chemical structure can help the understanding of these mechanisms. In this manuscript, we present our work on the complete structural characterization of the lipid A obtained from the lipopolysaccharides (LPS) of the haloalkaliphilic bacterium Salinivibrio sharmensis. Lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different number of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of electrospray ionization Fourier transform ion cyclotron (ESI FT-ICR) mass spectrometry and chemical analysis.

Valorisation of hydrothermal liquefaction wastewater in agriculture: effects on tobacco plants and rhizosphere microbiota.

Industrial wastewater obtained from hydrothermal liquefaction (HTL-WW) of food wastes for biofuels production could represent a source of crop nutrients since it is characterized by a high amount of organic and inorganic compounds. In the present work, the potential use of HTL-WW as irrigation water for industrial crops was investigated. The composition of the HTL-WW was rich in nitrogen, phosphorus, and potassium with high level of organic carbon. A pot experiment with Nicotiana tabacum L. plants was conducted using diluted wastewater to reduce the concentration of some chemical elements below the official accepted threshold values. Plants were grown in the greenhouse under controlled conditions for 21 days and irrigated with diluted HTL-WW every 24 hours. Soils and plants were sampled every seven days to evaluate, over time, the effect of wastewater irrigation both on soil microbial populations, through high-throughput sequencing, and plant growth parameters, through the measurement of different biometric indices. Metagenomic results highlighted that, in the HTL-WW treated rhizosphere, the microbial populations shifted via their mechanisms of adaptation to the new environmental conditions, establishing a new balance among bacterial and fungal communities. Identification of microbial taxa occurring in the rhizosphere of tobacco plants during the experiment highlighted that the HTL-WW application improved the growth of Micrococcaceae, Nocardiaceae and Nectriaceae, which included key species for denitrification, organic compounds degradation and plant growth promotion. As a result, irrigation with HTL-WW improved the overall performance of tobacco plants which showed higher leaf greenness and increased number of flowers compared to irrigated control plants. Overall, these results demonstrate the potential feasibility of using of HTL-WW in irrigated agriculture.

Fungal Biodeterioration and Preservation of Miniature Artworks.

The study of biodeterioration is an important issue to allow the best conservation and prevent the decay of cultural heritage and artworks. In Naples (Italy), a particular museum (Museodivino) preserves the miniature artworks representing Dante's Divine Comedy and Nativity scenes, executed with organic-based materials in walnut and clay shells. Since they showed putative signs of biodeterioration, the first aim of this study was to verify the presence of microbial colonization. A culture-dependent approach and molecular biology allowed us to isolate and identify the sole fungal strain Aspergillus NCCD (Nativity and Dante's Divine Comedy) belonging to the A. sydowii sub-clade. Based on this result, a sustainable and eco-friendly approach was applied to find a method to preserve the miniature artwork by contrasting the growth of the strain NCCD. Several essential oils used as a natural biocide were tested against Aspergillus strain NCCD belonging to the A. sydowii subclade to determine their potential antimicrobial activity. Results revealed that basil, cloves, fennel, and thyme essential oils exerted antifungal activity, although their effect depended also on the concentration used. Moreover, anoxic treatment and the control of the relative humidity were used in the presence of thyme, in vitro, and in vivo assays to define the impact on fungal growth. No fungal development was detected in vivo in the shells treated with thyme essential oil at high relative humidity after 60 days of incubation at 28 °C. These results highlighted that although relative humidity was the major factor affecting the development of the strain Aspergillus NDDC, the application of thyme in an anaerobic environment is essential in contrasting the fungal growth. Identifying the biodeterioration agent allowed us to plan an eco-friendly, non-destructive approach to be successfully used to guarantee the conditions suitable for conserving miniature artwork.

Impact of conservation tillage on wheat performance and its microbiome.

Winter wheat is an important cereal consumed worldwide. However, current management practices involving chemical fertilizers, irrigation, and intensive tillage may have negative impacts on the environment. Conservation agriculture is often presented as a sustainable alternative to maintain wheat production, favoring the beneficial microbiome. Here, we evaluated the impact of different water regimes (rainfed and irrigated), fertilization levels (half and full fertilization), and tillage practices (occasional tillage and no-tillage) on wheat performance, microbial activity, and rhizosphere- and root-associated microbial communities of four winter wheat genotypes (Antequera, Allez-y, Apache, and Cellule) grown in a field experiment. Wheat performance (i.e., yield, plant nitrogen concentrations, and total nitrogen uptake) was mainly affected by irrigation, fertilization, and genotype, whereas microbial activity (i.e., protease and alkaline phosphatase activities) was affected by irrigation. Amplicon sequencing data revealed that habitat (rhizosphere vs. root) was the main factor shaping microbial communities and confirmed that the selection of endophytic microbial communities takes place thanks to specific plant-microbiome interactions. Among the experimental factors applied, the interaction of irrigation and tillage influenced rhizosphere- and root-associated microbiomes. The findings presented in this work make it possible to link agricultural practices to microbial communities, paving the way for better monitoring of these microorganisms in the context of agroecosystem sustainability.

Inoculation with a microbial consortium increases soil microbial diversity and improves agronomic traits of tomato under water and nitrogen deficiency.

Microbial-based biostimulants, functioning as biotic and abiotic stress protectants and growth enhancers, are becoming increasingly important in agriculture also in the context of climate change. The search for new products that can help reduce chemical inputs under a variety of field conditions is the new challenge. In this study, we tested whether the combination of two microbial growth enhancers with complementary modes of action, Azotobacter chroococcum 76A and Trichoderma afroharzianum T22, could facilitate tomato adaptation to a 30% reduction of optimal water and nitrogen requirements. The microbial inoculum increased tomato yield (+48.5%) under optimal water and nutrient conditions. In addition, the microbial application improved leaf water potential under stress conditions (+9.5%), decreased the overall leaf temperature (-4.6%), and increased shoot fresh weight (+15%), indicating that this consortium could act as a positive regulator of plant water relations under limited water and nitrogen availability. A significant increase in microbial populations in the rhizosphere with applications of A. chroococcum 76A and T. afroharzianum T22 under stress conditions, suggested that these inoculants could enhance soil microbial abundance, including the abundance of native beneficial microorganisms. Sampling time, limited water and nitrogen regimes and microbial inoculations all affected bacterial and fungal populations in the rhizospheric soil. Overall, these results indicated that the selected microbial consortium could function as plant growth enhancer and stress protectant, possibly by triggering adaptation mechanisms via functional changes in the soil microbial diversity and relative abundance.

Extremophilic Microorganisms for the Green Synthesis of Antibacterial Nanoparticles.

The biogenic synthesis of nanomaterials, i.e., synthesis carried out by means of living organisms, is an emerging technique in nanotechnology since it represents a greener and more eco-friendly method for the production of nanomaterials. In this line, in order to find new biological entities capable of biogenic synthesis, we tested the ability of some extremophilic microorganisms to carry out the biogenic production of AgNPs and SeNPs. Silver NPs were produced extracellularly by means of the thermophilic Thermus thermophilus strain SAMU; the haloalkaliphilic Halomonas campaniensis strain 5AG was instead found to be useful for the synthesis of SeNPs. The structural characterization of the biogenic nanoparticles showed that both the Ag and Se NPs possessed a protein coating on their surface and that they were organized in aggregates. Moreover, both types of NPs were found be able to exert an interesting antibacterial effect against either Gram-positive or Gram-negative species. This study confirmed that extremophilic microorganisms can be considered valuable producers of biologically active nanoparticles; nevertheless, further experiments must be performed to improve the synthesis protocols in addition to the downstream processes.

Effects of Ionizing Radiation and Long-Term Storage on Hydrated vs. Dried Cell Samples of Extremophilic Microorganisms.

A main factor hampering life in space is represented by high atomic number nuclei and energy (HZE) ions that constitute about 1% of the galactic cosmic rays. In the frame of the "STARLIFE" project, we accessed the Heavy Ion Medical Accelerator (HIMAC) facility of the National Institute of Radiological Sciences (NIRS) in Chiba, Japan. By means of this facility, the extremophilic species Haloterrigena hispanica and Parageobacillus thermantarcticus were irradiated with high LET ions (i.e., Fe, Ar, and He ions) at doses corresponding to long permanence in the space environment. The survivability of HZE-treated cells depended upon either the storage time and the hydration state during irradiation; indeed, dry samples were shown to be more resistant than hydrated ones. With particular regard to spores of the species P. thermantarcticus, they were the most resistant to irradiation in a water medium: an analysis of the changes in their biochemical fingerprinting during irradiation showed that, below the survivability threshold, the spores undergo to a germination-like process, while for higher doses, inactivation takes place as a consequence of the concomitant release of the core's content and a loss of integrity of the main cellular components. Overall, the results reported here suggest that the selected extremophilic microorganisms could serve as biological model for space simulation and/or real space condition exposure, since they showed good resistance to ionizing radiation exposure and were able to resume cellular growth after long-term storage.