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March 2000 - February 2017
Publications
Publications (86)
Climate change has strongly increased the fire frequency in Mediterranean forests causing changes in soil bacterial, fungal and microarthropod communities. Fire impacts on soil properties depend on vegetation covers. In this framework, the aim of this research was to evaluate the effects of fire on bacterial, fungal communities and microarthropod c...
The Mediterranean area is a fragile semi-arid ecosystem, characterized by a high level of biodiversity. Due to its climatic conditions, fires are frequent. Fires strongly impact the microbial community of the soil and the biogeochemical cycles of the ecosystem. Although the N cycle is crucial, limited data is available about the effects of fires on...
The implementation of environmentally‐friendly agricultural policies has increased the need to compare agricultural aspects of conventional (CON) and organic farming (ORG) systems. The objective of the present work was to compare the effects of an organic and conventional long‐term experiment on bacterial and fungal biomass and activity, as well as...
Background
The concept of core-microbiome in health is useful for investigating the possible role of the oral microbiome in autoimmune disease, such as Rheumatoid Arthritis, Spondyloarthritis, Sjogren Syndrome or Systemic Sclerosis (SSc), whose pathogenesis has not been fully understood. Environmental factors and certain genetic backgrounds have be...
In systemic sclerosis (SSc), the gastrointestinal tract (GIT) plays a central role in the patient’s quality of life. The microbiome populates the GIT, where a relationship between the Lactobacillus and gastrointestinal motility has been suggested. In this study, the analysis of oral Lactobacillus species in SSc patients and healthy subjects using c...
Environmental DNA is made-up of intracellular (iDNA) and extracellular (eDNA) pools. In soils, eDNA can be present up to 40% and could distort the assessment of living microorganisms. Distribution of microbial community is inconsistent among different size-aggregates, and the persistence and turnover of eDNA are thus uneven. Uneven persistence and...
The combined action of physical protection and chemical stabilisation is the main factor regulating the persistence of soil organic matter (SOM). In particular, physical protection refers to the compartmentalization of SOM and microbial biomass within aggregates. Thus, we have investigated the role of (macro-, meso-and micro-) soil aggregates in th...
It is essential to investigate to which extent and how specifically soil-plant-microbe interactions can be conditioned by different agricultural practices. Legumes such as Vicia faba is one of the essential functional group in intercropping and crop rotations due to its higher N fixing capacity. Hence, it is important to study the living microbial...
The fate, properties and determination of microplastics (MPs) and nanoplastics (NPs) in soil are poorly known. In fact, most of the 300 million tons of plastics produced each year ends up in the environment and the soil acts as a log-term sink for these plastic debris. Therefore, the aim of this review is to discuss MP and NP pollution in soil as w...
Since the advent of sequencing technologies, the determination of microbial diversity to predict microbial functions, which are the major determinants of soil functions, has become a major topic of interest, as evidenced by the 900 publications dealing with soil metagenome published up to 2017. However, the detection of a gene in soil does not mean...
The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded...
In the last decades, many studies were addressed to focus the interplay between plant and microbial community into the soil and especially in the small soil zone in contact to plant root, called rhizosphere, which can be considered as a hotspot for interactions and therefore is a major target for improving nutrient use efficiency in crops. In this...
The intensive wildfires recurring in the Mediterranean area modify soil physico-chemical properties, in turn inducing changes in soil microbial abundance and activity. Soils were sampled from burnt and adjacent unburnt sites within Vesuvius National Park 1 year after a large wildfire occurred in summer 2017. The aims of the present study were to ev...
Wildfires are a driving factor of forest soils and their biota, especially in fire-prone ecosystems. Fire effects on soil microbial community are complex and still largely unknown. Greater knowledge is needed as fire frequency is expected to increase with human-induced climate change. This study aims at assessing the effects of a single moderately...
Introduction: The Mediterranean Diet (MD) is useful in the prevention of overweight, obesity and metabolic disease. High Quality-Extra Virgin Olive Oil (HQ-EVOO), an essential component of this diet, exerts protective effects against chronic diseases. Gut Microbiota (GM), recognized as a key factor in driving metabolic activities, is involved in th...
Several textbooks and edited volumes are currently available on general soil fertility but‚ to date‚ none have been dedicated to the study of “Sustainable Carbon and Nitrogen Cycling in Soil.” Yet this aspect is extremely important, considering the fact that the soil, as the ‘epidermis of the Earth’ (geodermis)‚ is a major component of the terrestr...
Jenull (2018) Chemical and microbiological changes in Norway spruce deadwood during the early stage of decomposition as a function of exposure in an alpine setting, Arctic, Antarctic, and Alpine Research, 50:1, e1438347 To link to this article: https://doi. ABSTRACT Alpine ecosystems are vulnerable to ever-changing environmental conditions, leading...
Pharmaceutical antibiotics are frequently used in the livestock and poultry industries to control infectious diseases. Due to the lack of proper guidance for use, the majority of administrated antibiotics and their metabolites are excreted to the soil environment through urine and feces. In the present study, we used chlortetracycline and sulfapyri...
Ascorbic acid is a bacteriostatic agent; one of the many ways by which ascorbic acid hampers bacterial growth is by the production of hydrogen peroxide, which further converts into hydroxyl free radicals. Certain amino acids can counteract the inhibitory effect of hydroxyl free radicals by checking their oxidizing effect. Though ascorbic acid is ba...
Oxytetracycline (OTC) and sulfamethoxazole (SMX) are two of most widely used antibiotics in livestock and poultry industry. After consumption of antibiotics, a major portion of these compounds is excreted through the feces and urine of animals. Land application of antibiotic-treated animal wastes has caused increasing concern about their adverse ef...
Although slope aspect determines the amount of solar irradiation, with implications on the functioning of forest ecosystems, little is known yet about how this affects the aboveground deadwood decomposition dynamics. Therefore, we set up a climosequence case study to evaluate the impact of slope exposure (north- vs. south-facing sites) on the physi...
Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme ac...
Cellulose is the most abundant polysaccharide in the dead plant biomass, and its degradation is an
important part of global carbon cycle. b-Glucosidases complete the final step of cellulose hydrolysis by
converting cellobiose to glucose. Genetic potential and expression of b-glucosidase genes were studied in
the topsoil of a Picea abies forest in t...
This study was carried out to understand the interplay of plant Nitrogen Utilizing Efficiency (NUE) with protease activity and microbial proteolytic community composition in the rhizosphere and bulk soils. Protease activity, diversity and abundance of protease genes (using DGGE and qPCR respectively of two key bacterial protease encoding genes: alk...
We studied the molecular diversity of β-glucosidase encoding genes, microbial biomass, cellulase, N-acetylglucosaminidase, β-glucosidase, and β-galactosidase activities in the rhizosphere and bulk soil of two maize lines differing in nitrogen use efficiency (NUE). The maize lines had significant differences in diversity of β-glucosidase-encoding ge...
Here we report a benchmark of the effect of bootstrap cut-off values of the RDP Classifier tool in terms of data retention along the different taxonomic ranks by using Illumina reads. Results provide guidelines for planning sequencing depths and selection of bootstrap cut-off in taxonomic assignments.
We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we iden...
To evaluate the effects of management practices and seasons on a soil bacterial community and the composition of ammonia-oxidizing bacteria (AOB), molecular screenings were compared among Mediterranean (Sardinia) soils with different plant covers and different agricultural practices, namely cork oak forest, tilled/non-tilled vineyard, hay crop and...
Aims
Study of the changes in soil microbial biomass, enzyme activity and the microbial community structure in the rhizosphere of two contrasting maize lines differing in the nitrogen use efficiency (NUE).
Methods
The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhiz...
We set up a simple, culture independent, low-cost and high-throughput method for DNA-based quantitative assessment of soil microbial biomass using eight soils covering a wide range of physico-chemical properties. DNA was extracted with a 0.12 M, pH 8 Na2HPO4 buffer using bead beating; double stranded DNA (dsDNA) was quantified in a crude (not purif...
Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurrence, and role of its different microbial populations are largely unknown. Here, two sterilized soils (from England and Italy) were inoculated with a subsample of their initial microbial communities and/or those from the other soil to study their microb...
In relation to climate change effects on forest ecosystem, the frequency of fire events represents one of the most drastically events that are expected to increase in the future, not only in the Mediterranean basin but also in not traditionally interested areas. The fire impact on soil ecosystem has been only recently considered in relation to its...
One of the most promising areas for future development is the
manipulation of the rhizosphere to produce sustainable and efficient
agriculture production systems. Using Omics approaches, to define the
distinctive features of eDNA systems and structures, will facilitate
progress in rhizo-enforcement and biocontrol studies. The relevance of
these stu...
Olive trees play an important role in cultural, ecological, environmental and social fields, constituting in large part the Mediterranean landscape. In Tuscany, an important economic activity is based on olive. Unfortunately, the Verticillium wilt affects this species and causes vascular disease. In the present study, a real-time quantitative PCR a...
We performed screening of bacteria inhabiting soil organic (O) layers vs mineral (A) layers. Community level and group-specific genetic fingerprinting was used to assess changes in bacterial structures of dry woodlands of Argentina as function of regional climate, season and land use. Multiple factor effects and correlations of soil organic matter,...
The aim of the study was to evaluate the impact of cattle overwintering husbandry on composition of upland grassland soil archaeal, bacterial, and fungal communities by comparative fingerprinting (SSU rRNA denaturing gra-dient gel electrophoresis (DGGE)) of total (tDNA) and extracellular DNA (eDNA) extracted from three differently impacted soils (s...
Global warming primarily affects topsoil processes such as organic matter turnover observable as changes of the humus form. We studied the influence of pedoclimate on the biological and morphological development of humus profiles in spruce forests on basaltic latite debris in the Southern Alps (Val di Fassa, Trentino, Italy). Four sites were select...
Global warming primarily affects topsoil processes such as organic matter turnover observable as changes of the humus form. We studied the influence of pedoclimate on the biological and morphological development of humus profiles in spruce forests on basaltic latite debris in the Southern Alps (Val di Fassa, Trentino, Italy). Four sites were select...
There is a growing interest in the links between humus forms and soil biota, and little is known about these links in Mediterranean ecosystems. Culture-independent techniques, such as DNA extraction followed by DGGE and enzyme activities, allowed us to compare microbial communities in two horizons of a forest soil in different seasonal conditions....
This study focuses on the biological and morphological development of humus profiles in forested Italian Alpine soils as a function of climate. Humus form description, systematic investigation of microannelid communities and polyphasic biochemical fingerprinting of soil microbial communities (denaturing gradient gel electrophoresis (DGGE) and phosp...
We compared two denaturing gradient gel electrophoresis (DGGE) systems—DCode (Biorad, Hercules, CA, USA) and PhorU (Ingeny,
Leiden, NL), performing community level 16S and 18S rRNA gene fragment-PCR-DGGE with total DNA extracted from upland pasture
soil used for outdoor cattle husbandry. The methodological evaluation of the DGGE apparatus as parame...
The long-term physical persistence and biological activity of transplastomic plant DNA (transgenes contained in the chloroplast genome) either purified and added to soil or naturally released by decaying tobacco leaves in soil was determined. Soil microcosms were amended with transplastomic tobacco leaves or purified plant DNA and incubated for up...
The soil genome consists of an intracellular and an extracellular fraction. Recently, soil extracellular DNA (eDNA) has been shown to be quantitatively relevant, with a high survival capacity and mobility, playing a crucial role in the gene transfer by transformation, in the formation of bacterial biofilm and as a source of nutrients for soil micro...
Unsaturated soil columns were used to examine the transport of the plasmid pLEPO1 and plant DNA (transplastomic tobacco DNA), both carrying an antibiotic resistance gene (aadA gene), and the capacity of bacteria to incorporate the gene in their genome after its passage through the soil. Soil columns containing a top leaf layer had sterile water per...
We experimentally discriminated and quali-quantitatively characterized the extracellular fraction of a forest soil DNA pool.
We sequentially extracted and classified the components of extracellular DNA by its strength of interaction with soil colloids
as: (1) extractable in water, free in the extracellular soil environment or adsorbed on soil collo...
Keywords:rhizosphere DNA;bt-maize;DNA movement;real-time PCR;TaqMan®.
The soil DNA pool consists of an intracellular (iDNA) and extracellular fraction (eDNA). Challenging to improve the extraction efficiency of soil DNA, and to quantitatively and qualitatively characterize both DNA fractions, we set up a molecular approach consisting of sequential and comparative DNA extraction and microbial community fingerprinting....
Beringite (B) and zerovalent iron grit (Z), singly and in combination (BZ), were added to a loamy sand soil contaminated by trace elements (Reppel, Belgium), mainly by arsenic (As), to reduce As labile fractions and phytoavailability. An uncontaminated sandy soil was studied for comparison. Soils were placed in large lysimeters cultivated with maiz...
This study addressed the possibility that DNA, like other organic molecules, could be transported in the soil water flow by vertical and horizontal advections. Using a soil column system, the movements of a DNA sequence not present in the soil DNA pool were monitored and quantified via real-time PCR. The target sequence, belonging to bt- maize MON8...
We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and activity, microbial and plant species richness, of an As-contaminated mine spoil, amended with compost (C) alone and in combination with beringite (B) or zerovalent iron grit (Z), to increase organic matter content and reduce trace elements mobility, an...
The review discusses origin, state and function of extracellular DNA in soils and sediments. Extracellular DNA can be released
from prokaryotic and eukaryotic cells and can be protected against nuclease degradation by its adsorption on soil colloids
and sand particles. Laboratory experiments have shown that DNA adsorbed by colloids and sand particl...
Research in soil microbiology has concerned the determination of the presence of gene sequences so as to assess microbial diversity rather than the determination of gene expression. Generally these molecular techniques are based on the specific amplification of the target nucleic acid by polymerase chain reaction (PCR) with either restriction analy...
The rhizosphere is the soil volume at the root-soil interface that is under the influence of the plant roots and the term was introduced by Hiltner in 1904 (Brimecombe et al. 2001). Microbial population in the rhizosphere has continuous access to a flow of low and high molecular weight organic substrates derived from roots. This continuous flow of...
The composition and activity of ammonia-oxidizing bacteria (AOB) in soil and tree-bark of a pine forest of Central Italy were investigated by molecular methods because it is known that soil pH is an important environmental factor structuring the soil macrofauna community in the tree vicinity, but, the effects of the stemflow on the composition of s...
The aim of this work was to study variations in the composition of eubacteria and ammonia-oxidizing populations of soil, both
determined by denaturing gradient gel electrophoresis (DGGE), after the addition of a pharmaceutical fungal biomass, treated
to degrade its DNA. This waste can be used as an amendment. The fungal biomass waste was added at t...
The aim of this work was to obtain pure extracellular DNA molecules so as to estimate their longevity in soil by an isotope-based approach. Extracellular DNA molecules were extracted from all horizons of a forest soil and purified by the procedure of Davis (Purification and precipitation of genomic DNA with phenol–chloroform and ethanol. In: Davis...
Several studies have investigated the adsorption of pure DNA on soil particles and its transformation ability. However, the presence of not purified (dirty) rather than pure DNA is more common in the extracellular soil environment. For this reason, we have investigated the adsorption
and binding of dirty DNA on montmorillonite (M) and kaolinite (K)...
The fate of extracellular DNA in the environment concerns both the fate of transgenes from genetically modified organisms and the evolution of active bacteria capable of incorporating this DNA into their genomes. This study addressed the possibility that DNA, like other organic molecules, could move vertically in the capillary fringe of groundwater...
The aim of this work was to study the synthesis and persistence of acid and alkaline phosphomonoesterases in three soils with different pH values amended with ryegrass residues. The organic input increased soil respiration, as estimated by CO2–C evolution in all soils. The ATP content of the three soils showed a 3–7-fold increase between 7 and 10d...
The study of the fate of transgenic and not transgenic extracellular DNA in soil is of extreme relevance because the soil extracellular DNA pool represents a genetic reservoir that could be utilized as a source of food by any heterotrophic microorganism or genetic information by recipient eukaryotic and prokaryotic cells. Several data have clearly...
We studied the distribution of the indigenous bacterial and fungal communities in a forest soil profile. The composition of bacterial and fungal communities was assessed by denaturing gradient gel electrophoresis (DGGE) of total and extracellular DNA extracted from all the soil horizons. Microbial biomass C and basal respiration were also measured...
Long-term effects of high Cd concentrations on enzyme activities, microbial biomass and respiration and bacterial community structure of soils were assessed in sandy soils where Cd was added between 1988 and 1990 as Cd(NO3)2 to reach concentrations ranging from 0 to 0.36 mmol Cd kg−1 dry weight soil. Soils were mantained under maize and grass culti...
Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme ac...
Interest in the fate of microorganisms (genetically modified or not) added to soil for a range of applications (e.g., biological fertilizer, bioremediation) has led to the examination of the transport and dispersion of bacteria in soil and ground water environments. The fate of added microorganisms can also be related to the fate of their DNA or an...
The fate of transplastomic (chloroplast genome contains the transgene) tobacco plant DNA in planta was studied when the plant leaves were subjected to decay conditions simulating those encountered naturally, including grinding, incubation with cellulase or enzymes produced by Erwinia chrysanthemi, and attack by the plant pathogen Ralstonia solanace...
Soil plays a fundamental and irreplaceable role in the biosphere because it gov- erns plant productivity of terrestrial ecosystem, allows the completion of the biogeochem- ical cycles and microorganisms inhabiting soil degrade, sooner or later, all organic com- pounds including those more recalcitrant. The main characteristics of soil are the domin...
Restriction analysis of amplified 16S rDNA from bacterial strains isolated from soil was used to evaluate the effects of swine manure and urea fertilisation on indigenous populations of the plant growth promoting bacterium, Azospirillum brasilense, in corn- cul- tivated experimental plots. Several operational taxonomic units (OTUs) were found among...
The effects of two weeding methods (I-chemical treatments on the open ground; 2-chemical treatment on rows integrated with hoeings) on respiratory activity, microbial biomass C, metabolic quotient (qCO(2)), organic C content, mineralization index, nitrate concentration and potential nitrification activity (PNA) have been evaluated in plot trials on...
Probes for the detection of Azospirillum strains were obtained from DNA fragments generated by random amplification of polymorphic DNA (RAPD) and tested to assess
their specificity towards DNA extracted from pure cultures. The most specific probe, referred to as α4, produced a hybridization
signal only with amplified DNA of A. lipoferum ATCC29731....
Molecular and biochemical investigation methods have been exploited to evaluate the effects of pig slurry, used for three years as a fertilizer in intensive agriculture, on the presence and activity of chemolithotrophic ammonia oxidizing bacteria, the biocatalysts of the first step in the nitrification process. The evaluation was carried out, on bu...
The application of pig slurry, high in ammonia-nitrogen concentration, to agricultural land is a practice whose effect on soil microbial communities is poorly understood. The autotrophic ammonia-oxidising bacteria are an integral component of the nitrogen cycle in soil, and their activity will be affected by addition of nitrogenous fertilizer. Mole...
The presence of chemoautotrophic ammonia axidizers was investigated with 16S rDNA oligonucleotides in cultivated and in 25 year uncultivated vertic cambisol plots, and their related potential nitrifying activity was evaluated. The data indicated that different agricultural practices do not affect this microbial population, while have an effect on t...
The 16S rDNA of 17 strains of Azospirillum, 14 assigned to one of the known species A. amazonense, A. brasilense, A. halopraeferens, A. irakense and A. lipoferum, and the other three of uncertain taxonomic position, was sequenced after polymerase chain reaction amplification and analysed in order to investigate the phylogenetic relationships at the...
