Stefano Mocali

• Council for Agricultural Research and Agricultural Economy Analysis

Archived soil series provide valuable opportunities to assess microbial temporal dynamics, which are essential for identifying appropriate soil management practices. However, the soil microbiome is usually studied using cryopreserved fresh soils, while almost all archived soils are dry and stored at room temperature. The aims of the present study w...

Comparability of soil data derived from different sources is crucial to obtain consistent results when evaluating the soil health status. Discrepancies may arise due to various factors, including uncertainties resulting from different sampling methods. In this study, we compared various soil Physicochemical properties (ST)—pH, organic carbon, textu...

The loss of organic matter and the decline of biodiversity pose significant threats to soil health and the sustainability of agriculture. Managing set-aside land through mowing remains a practical strategy to prevent land abandonment while preserving soil biodiversity and essential soil functions that support fertility. The primary objective of thi...

Salinity is one of the main abiotic stresses that limits plant growth. This study addressed how the composition and diversity of root-associated bacterial communities reacts over time to salt-induced stress conditions. To understand its adaptation to soil salinization, the microbiome was studied by total DNA extraction and sequencing, using the Ill...

The understanding of selective forces driving the compartmentalization of microbiota in plants remains limited. In this study, we performed a phenotypic characterization of bacterial endophytes isolated from the medicinal plant Origanum heracleoticum, together with the determination of the antibiotic resistance profiles and the antagonistic interac...

Antibiotic resistance (AR) is recognized by the World Health Organization as a major threat to human health, and recent studies highlight the role of microplastics (MPs) in its spread. MPs in the environment may act as vectors for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Bacterial communities on the plastisphere,...

Background: Self-organizing maps (SOMs) are a class of neural network algorithms able to visually describe a high-dimensional dataset onto a two-dimensional grid. SOMs were explored to classify soils based on an array of physical, chemical, and biological parameters. Methods: The SOM analysis was performed considering soil physical, chemical, and m...

In the last years, different biotechnological approaches were developed to reduce the indiscrimi-nate use of chemical fertilizers and pesticides and enhance plant growth and health. The most at-tractive, safe, and environmentally mild alternatives include those based on plant beneficial mi-croorganisms. After a long period of studies on isolation,...

Vine growing is one of the most economically important sectors of Mediterranean agriculture, but its cultivation practices are highly detrimental to the environment and the associated biota. The application of both natural products inducing endogenous plant defense mechanisms and natural soil management systems represents a potential solution for t...

Desert soil hosts many microorganisms, whose activities are essential from an ecological viewpoint. Moreover, they are of great anthropic interest. The knowledge of extreme environments microbiomes may be beneficial for agriculture, technology, and human health. In this study, 11 Arthrobacter strains from topsoil samples collected from the Great Go...

Understanding how microbial communities survive in extreme environmental pressure is critical for interpreting ecological patterns and microbial diversity. Great Gobi A Strictly Protected Area represents an intriguing model for studying the bacterial community since it is a protected and intact wild area of the Mongolian desert. In this work, the c...

In this chapter, we address a series of topics that have experienced a strong evolution or become important issues since 2000 to date in Italy. Topics range from (i) legislative acts that have affected soil science to (ii) the advancements in the fields of pedology, palaeosols, analytical methods, slush and burn, use of compost, and GIS to (iii) th...

Soil Science has always been a topic of considerable interest for CREA, the Council for Research in Agriculture and the Analysis of Agricultural Economics. From 1910 to today, CREA has contributed to the progress of Soil Science in its headquarters of Rome, Florence, Bari and Gorizia. For a systematic narration of CREA’s contributions to soil scien...

Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applic...

Soil microbiota is a crucial component of agroecosystem biodiversity, improving plant growth and providing important services in agriculture. However, its characterization is demanding and expensive. In this context, cross-taxon analyses are useful to detect organisms that are surrogates of other taxonomic groups. Here, we evaluated whether arable...

Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant’s microenvir...

Cross-taxon analyses are important to detect organisms that are surrogates of other components of biodiversity. However, multi-taxonomic surveys can be challenging, expensive and time-consuming. To our knowledge, no studies investigated cross-taxon congruence between vascular plant and soil microbial communities in arable ecosystems. Thus, in this...

Aims: The increasingly widespread use of beneficial microbial inocula in agriculture gives rise to two primary needs: i) the assessment of the environmental risk, i.e. their impact on local soil microbiome and soil properties; ii) being able to track them and monitor their persistence and fate to both optimize their formulation and application met...

The application of plant beneficial microorganisms is widely accepted as an efficient alternative to chemical fertilizers and pesticides. It was shown that annually, mycorrhizal fungi and nitrogen-fixing bacteria are responsible for 5 to 80% of all nitrogen, and up to 75% of P plant acquisition. However, while bacteria are the most studied soil mic...

Healthy soils form the basis of sustainable viticulture, where soil characteristics have a direct impact on wine quantity and quality. Soil not only provides water and nutrients to vines, but is also a living medium containing micro- and macroorganisms that perform many ecological functions and provide ecosystem services. These organisms are involv...

The indiscriminate use of chemical fertilizers adversely affects ecological health and soil microbiota provoking loss of soil fertility and greater pathogen and pest presence in soil-plant systems, which further reduce the quality of food and human health. Therefore, the sustainability, circular economy, environmental safety of agricultural product...

Soil microorganisms are key drivers of soil biochemical processes, but the resilience of microbial communities and their metabolic activity after an extreme environmental change is still largely unknown. We studied structural (bacterial and fungal communities) and functional responses (soil respiration, adenosine triphosphate (ATP) content, hydrola...

Maintaining or recovering soil health is becoming a goal of many policies carried out at national, continental and global scales to promote global health. This viewpoint is aimed at stressing the relevance of a holistic approach to soil health assessment and monitoring, which is not only related to soil functional biodiversity but also considers th...

Plant protection strategies in organic viticulture are based on the application of copper products, which is well known to generate a consistent environmental impact due to the accumulation of copper in soils and its negative effects on edaphic biodiversity. Life Green Grapes is a demonstrative project aiming to improve the sustainability of viticu...

Biodiversity maintenance is a key strategy for sustainable forestry in both above-ground and below-ground biotic communities. However, few studies applied continuous monitoring to analyse the responses of different taxonomic groups to silvicultural treatments. We studied the short-term effects of three silvicultural treatments (no thinning, thinni...

Microbial inoculants can be an efficient tool to manage the soil and plant microbiomes providing direct beneficial effects, and for modulating native soil and plant-associated microbiota. However, the application of soil microbial inoculants as biofertilizers and biopesticides in agriculture is still limited by factors related to their formulation,...

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 m...

The use of biowaste compost as soil organic amendment is of great interest for soil recovery. However, there is little knowledge of detailed effects on chemical, microbial, and biochemical properties in different soil compartments (aggregate classes) following long-term amendment with biowaste compost. We studied the distribution of soil organic ca...

The application of plant beneficial microorganisms has been widely accepted as an efficientalternative to chemical fertilizers and pesticides. Isolation and selection of efficient microorganisms,their characterization and testing in soil-plant systems are well studied. However, the productionstage and formulation of the final products are not in th...

The application of plant beneficial microorganisms has been widely accepted as an efficient alternative to chemical fertilizers and pesticides. Isolation and selection of efficient microorganisms, their characterization and testing in soil-plant systems are well studied. However, the production stage and formulation of the final products are not in...

The aim of the present experiment was to determine if the supply of biofertilizers could differently stimulate the native microbiota, thus determining different patterns of organic material decomposition processes. The microbial composition of soil and litter was investigated by next generation sequencing using a metabarcoding approach. The chemica...

Biodiversity maintenance is a key strategy for sustainable forestry in both above-ground and below-ground biotic communities. However, few studies applied continuous monitoring to analyse the responses of different taxonomic groups to silvicultural treatments. We studied the short-term effects of three silvicultural treatments (no thinning, thinnin...

Monosporascus root rot and vine decline of melon (MRRVD) is a destructive disease complex mainly occurring in semiarid cultivation areas. In the last decade, in the melon producing area of Sardinia (Italy), yield reductions up to 100% were recorded due to the occurrence of MRRVD. The present study aimed to undertake a two-year survey of fungal path...

Microbial inoculants are widely accepted as potential alternatives or complements to chemical fertilizers and pesticides in agriculture. However, there remains a lack of knowledge regarding their application and effects under field conditions. Thus, a quantitative description of the scientific literature related to soil microbial inoculants was con...

The Italian regulatory framework on genetically modified organisms (GMOs) follows the cardinal principles of the European Union legal order. The incomplete implementation of the Italian legislation has led to a de facto moratorium of the deliberate releases of GMOs into the environment, also for experimental purposes , thus slowing down the Italian...

The quality of the vineyard soils has a direct impact on grapes and wine quality and represents a key component of the “Terroir concept.” However, information on the impact of soil microbiota on grapevine plants and wine quality are generally lacking. In fact, over the last few years most of the attempts made to correlate soil microbial communities...

Acquarossa river (Viterbo, Italy) was the site of a prospering Etruscan civilization thanks to metallurgical activity around 625–550 B.C. This caused the spread of heavy metals throughout the area. Rocks along the river probably act as a filter for these elements and they are covered by two different biofilms (epilithons). They differ for both colo...

The antagonistic interactions between microorganisms in the environment seem to play a key role in determining the spatial structuring of bacterial communities. In this work, the antagonistic interactions among 82 strains belonging to different Pseudomonas species isolated from six different environmental niches have been investigated to check whet...

Soil plays a fundamental role in many ecological processes, throughout a complex network of above- and below-ground interactions. This has aroused increasing interest in the use of correlates for biodiversity assessment and has demonstrated their reliability with respect to proxies based on environmental data alone. Although co-variation of species...

Soil magnetic properties are sensitive indicators of pedogenetic processes. Although many of the processes that increase soil magnetism are well documented, the role of microbial communities and the metabolic characteristics of Fe-reducing bacteria are still largely unknown. For this work, two soils with contrasting magnetic properties were identif...

To test the robustness of cross-taxon congruence across different groups of organisms (bacteria, carabids, ectomycorrhizae, microarthropods, mushrooms, mycelium, nematodes, vascular plants); to assess how abiotic (soil and spatial-topographic) and biotic (dendrometric) predictors drive the community concordances among taxa; - to explore ecological...

A key factor in the study of plant-microbes interaction is the composition of plant microbiota, but little is known about the factors determining its functional and taxonomic organization. Here we investigated the possible forces driving the assemblage of bacterial endophytic and rhizospheric communities, isolated from two congeneric medicinal plan...

The current Common Agricultural Policy (CAP) 2014-2020 of the European Union (EU) proposed some environmental attempts to contrast the biodiversity decline and mitigate the effects of intensive agricultural management systems. In the present work, the results of the effectiveness of set-aside management to enhance soil nematode biodiversity and soi...

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about mi...

The LIFE Projects SelPiBio (LIFE13 BIO/IT/000282 ”Innovative silvicultural treatments to enhance soil Biodiversity in artificial black Pine stands”) and FoResMit (LIFE14 CCM/IT/000905 ”Recovery of degraded coniferous Forests for environmental sustainability Restoration and climate change Mitigation”) are two Italian projects aimed at testing and ve...

Cold environments dominate Earth’s biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacte...

Burkholderia cepacia complex bacteria (Bcc) represent a serious threat for immune-compromised patient affected by Cystic Fibrosis (CF) since they are resistant to many substances and to most antibiotics. For this reason, the research of new natural compounds able to inhibit the growth of Bcc strains has raised new interest during the last years. A...

Dredged sediments have currently no broad reuse options as compared to other wastes due to their peculiar physico-chemical properties, posing p roblems for the management of the large volumes of sediments dredged worldwide. In this study we evaluated the performance of sediment (S) co-composted with green waste (GW) as growing medium for ornamental...

The main goal of the SelPiBioLife project is to demonstrate how an innovative silvicultur- al treatment applied to pine forests of Pinus nigra J.F. Arnold could increases biodiversity of the various soil components (flora, fungi, bacteria, mesofauna, nematods). In particular, we evaluated the effects on the forest functionality (both productive and...

In the symbiosis between rhizobia and legumes, host plants can form symbiotic root nodules with multiple rhizobial strains, potentially showing different symbiotic performances in nitrogen fixation. Here, we investigated the presence of mixed nodules, containing rhizobia with different degrees of mutualisms, and evaluate their relative fitness in t...

Effect of strain competition on host plants. (A) Nodulation index. Percentage of nodulated plants for single and mixed strains combinations. Values are means (śstandard deviation) of three independent experiments, each involving at least 20 plants. (B) Nodulation score. Mean number of nodules/plant. Values indicate means ś standard deviation of num...

Input data and code used to generate the figures.

Number of copies of the genome/nodule of the qPCR estimates in the in vivo experiment. The plants were inoculated with the wild type strains. Measurements were performed on three nodules for each mixed inoculum.

Commercially available lyophilized microbial standards are expensive and subject to reduction in cell viability due to freeze-drying stress. Here we introduce an inexpensive and straightforward method for in-house microbial standard preparation and cryoconservation that preserves constant cell titre and cell viability over 14 months.

Different bacteria have evolved strategies to transfer electrons over their cell surface to (or from) their extracellular environment. This electron transfer enables the use of these bacteria in bioelectrochemical systems (BES) such as Microbial Fuel Cells (MFCs). In MFC research the biological reactions at the cathode have long been a secondary po...

The advantage of a pot system is the possibility to control many variables and factors with a large number of replicates, obtaining statistically significant results in only one year of experimentation. An innovative pot system for the monitoring of grapevine water stress was set up. The system consists of 99 pots of 70 liters, filled by 3 differen...

In 2005, the CAP reform introduced the principle of conditionality that enables the access to single payments for farmers only ‘on condition’ that a series of commitments, such as the Statutory Management Requirements (SMR) and Good Agricultural and Environmental Conditions (GAEC), are respected. In particular, the GAEC Standard 4.2 aims to ensure...

The application of pelletized biochar is seldom employed in field, and its effect on soil hydrological behaviour scarcely investigated. Biochar is usually added in powdered or granular form to improve the homogeneity of distribution, meanwhile favouring its interaction with soil matrix. In this study we evaluated the possibility of applying pelleti...

One of the main consequence of intensive forest exploitation, overgrazing and recurring wildfires over the centuries is the decay of forest cover and soil erosion. In many areas of the Italian Apennines, Black pine (Pinus nigra Arn.) plantations were established after the Second World War to improve forest soil quality in marginal and eroded soils....

The data presented in this work are part of a LIFE Biodiversity project (SELPIBIOLIFE) presented by 5 partners with the main goal to demonstrate the positive effects of an innovativesilvicultural treatment on black pine forests. The specific management applied improves growth rates and stands stability and enhance the level of biodiversity of vario...

In the present contribution are presented the main activities and objectives of the LIFE13 BIO/IT/000282 Project SelPiBioLife-Innovative silvicultural treatments to enhance soil biodiversity in artificial black pine stands, coordinated by the Research Centre for Forest Ecology and Silviculture (CRA-SEL) of the Council for Agricultural Research and...

We studied how the Lo5 and T250 maize lines, characterized by high and low Nitrogen Use Efficiency (NUE), respectively, modified the microbial biomass, enzymatic activities and microbial community structure in the rhizosphere after exposure to different N forms. The two maize lines were grown for 4 weeks in rhizoboxes allowing precise sampling of r...

Short-term recovery of soil physical, chemical, microand mesobiological functions in a new vineyard under organic farming

The replacement of chemical pesticides with alternative biocidal compounds after the Directive 2009/128/EC increased a renewed interest in biofumigation. Defatted seed meals (DSMs) derived from brassicaceae plant tissues with high glucosinolate content represent an alternative to control soil-born plant pathogens and pests, such as nematodes, and c...

Deep earthwork activities carried out before vineyard plantation can severely affect soil profile properties. As a result, soil features in the root environment are often much more similar to those of the underlying substratum than those of the original profile. The time needed to recover the original soil functions is ecologically relevant and may...

One of the main consequence of intensive forest exploitation, overgrazing and continual wildfires over the centuries is the decay of forest cover and soil erosion. In various areas of the Italian Apennines, Black pine plantations were established after the Second World War to improve forest soil quality in marginal and eroded soils. The main aim of...

Notions of terroir and their conceptualization through agro-environmental sciences have become popular in many parts of world. Originally developed for wine, terroir now encompasses many other crops including fruits, vegetables, cheese, olive oil, coffee, cacao and other crops, linking the uniqueness and quality of both beverages and foods to the e...

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...

The ability to relate genomic differences in bacterial species to their variability in expressed phenotypes is one of the most challenging tasks in today’s biology. Such task is of paramount importance towards the understanding of biotechnologically relevant pathways and possibly for their manipulation. Fundamental prerequisites are the genome-wide...

In this work we analyzed the composition and structure of cultivable bacterial communities isolated from the stem/leaf and root compartments of two medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC.) Hell, grown in the same soil, as well as the bacterial community from their rhizospheric soils. Molecular PCR-based tech...