Francesca Decorosi

Plastic mulching provides clear benefits for strawberry cultivation but pose risks of long-term environmental pollution. However, a comprehensive investigation on how different plastic materials may impact the overall strawberry cultivation, from soil health to crop productivity, is lacking. This study investigates the influence of conventional and degradable mulching films on substrate microbial ecology, concurrently evaluating plant performance and fruit quality in a strawberry cultivation. Different mulch films were applied and compared to unmulched control: polyethylene (PE), oxo-degradable (OxoPE), polybutylene adipate terephthalate corn starch-blended (PBAT), polypropylene (PP). Substrate physicochemical analysis and 16S rRNA gene high-throughput sequencing were performed, along with plant morphological and physiological analysis, strawberries yield and quality. PBAT promotes substrate nitrogen enrichment, whereas PE induced an increase in available micronutrients. Bacterial community α-diversity increased in the presence of OxoPE, PE, and PP films, while β-diversity analysis revealed a distinct clustering based on film type, with the biodegradable PBAT communities separating from the others materials. This separation was driven by gradients of humidity and nitrate, with OxoPE, PE, and PP communities positively correlated with higher humidity. Functional predictions suggest that PE mulches boost nitrogen-fixing communities, whereas PBAT promotes nitrification and complex carbon catabolism. At plant level, OxoPE and PP significantly increased fruit yield up to 29% compared to the control, while physiological and growth traits remained consistent across treatments, as well as fruit quality and nutraceutical properties. This study demonstrates that distinct mulches uniquely promote substrate biodiversity by shaping specialized, functional bacterial communities.

At the archeological site of Pompeii, the deterioration of exposed structures is frequently associated with the combined action of microbial colonization and soluble salts, both recognized as major agents of decay affecting ancient surfaces. Although biocides are commonly applied during cleaning procedures to reduce microbial biomass, their incorporation into restoration-oriented formulations for the protection of porous stone substrates requires careful assessment of efficacy, microbiological risks, and sustainability. This study evaluated the performance of 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil) and iodopropynyl butylcarbamate (IPBC) as candidate active ingredients for conservation applications in activated new mortars. Yellow tuff, gray tuff, and brick samples collected from different sectors of Pompeii were investigated through culture-based analyses, ATP quantification, and metabolic profiling. Biocidal treatments were subsequently tested under laboratory conditions. The investigated substrates exhibited variable microbial counts and metabolic activity, generally reflecting different degrees of deterioration. Chlorothalonil showed negligible inhibitory effects, whereas IPBC reduced fungal growth in a dose-dependent manner. However, the highest IPBC concentration induced a red chromatic alteration associated with the selection of a bacterial strain preliminarily identified as Micrococcus roseus. Phenotype microarray analyses revealed broad chemical tolerance. Overall, biocidal treatments may alter microbial communities, favor tolerant microorganisms, and produce undesirable aesthetic effects. Finally, the study also assessed the environmental impact associated with laboratory and field activities, highlighting potential mitigation strategies to support more sustainable conservation research practices.

Soil salinity poses a major challenge to the legume‐rhizobia symbiosis development, thereby affecting sustainable agriculture. Selecting NaCl‐tolerant strains and enhancing the native strains' fitness under salt stress are essential steps for the restoration of marginal areas. In this work, 49 Sinorhizobium meliloti strains, the rhizobial species forming symbiotic nitrogen‐fixing associations with alfalfa—including 21 de novo‐sequenced field isolates—were subjected to a thorough in vitro screening for salt tolerance at progressively higher NaCl concentrations. Field isolates showed genome‐based geographical clustering but contrasting salt tolerance abilities. Indeed, genome‐wide association (GWA) analysis on the strains' whole‐genome sequencing data indicated several loci associated with the variability in salt tolerance. Candidate genes were involved in various processes including cell wall organisation, LPS biosynthesis, quorum sensing, and carbohydrate transport and metabolism. The relationship with carbohydrate metabolism was further confirmed by Phenotype Microarray analysis which indicated salt‐tolerant strains having enhanced capacity in carbon source usage. These findings reveal synergistic pathways underlying salt tolerance and suggest candidate traits (e.g., quorum sensing, carbohydrate synthesis and modification) for developing bioinoculants to enhance legume performance in saline soils.

A corrigendum of this article has been published full details can be found at 10.1099/ijsem.0.007033 We present the description of the new species, Rhodococcus parequi , found during phylogenomic investigations of a global collection of strains identified as Rhodococcus ( Prescottella ) equi . Strain PAM 2766 ^T was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from R. equi based on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766 ^T in the same Rhodococcus sublineage as R. equi , together with Rhodococcus agglutinans , Rhodococcus defluvii , Rhodococcus soli , Rhodococcus subtropicus , Rhodococcus spongiicola and Rhodococcus xishaensis . PAM 2766 ^T is most closely related to, but sufficiently distinct from, R. equi DSM 20307 ^T to be considered a separate species. The average nt identity (ANI) and average aa identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766 ^T draft genome is ~5.3 Mb in size with 68.98% G+C mol content. PAM 2766 ^T is strictly aerobic and non-motile and produces smooth, creamy to buff-coloured colonies very similar to those of R. equi . It phenotypically differs from the latter by the ability to grow at 5 °C, a strongly positive urease test at 24 h and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766 ^T belongs to a novel species, for which the name Rhodococcus parequi sp. nov. is proposed. R. parequi was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766 ^T (=CETC 30995 ^T =NCTC 14987 ^T ).

Slow decomposition rates of cereal crop residues can lead to agronomic challenges, such as nutrient immobilization, delayed soil warming, and increased pest pressures. In this regard, microbial inoculation with efficient strains offers a viable and eco-friendly solution to accelerating the decomposition process of crop residues. However, this solution often focuses mostly on selecting microorganisms based on the appropriate enzymic capabilities and neglects the metabolic versatility required to utilize both structural and non-structural components of residues. Therefore, this study aimed to address these limitations by assessing the metabolic profiles of five previously identified cellulolytic bacterial strains, including Bacillus pumilus 1G17, Micromonospora chalcea 1G49, Bacillus mobilis 5G17, Streptomyces canus 1TG5, and Streptomyces achromogenes 3TG21 using Biolog Phenotype Microarray analysis. Moreover, this study evaluated the impact of wheat straw inoculation with single strains and a bacterial consortium on soil organic carbon and nitrogen content in a pot experiment. Results revealed that, beyond the core subset of 12 carbon sources, the strains exhibited diverse metabolic capacities in utilizing 106 carbon sources. All strains demonstrated effective straw biomass degradation compared to the negative control, with significant differences detected only in oil seed rape straw biodegradation estimations. Furthermore, wheat straw inoculated with a bacterial consortium showed a significant increase in soil organic carbon content after 180 days in the pot experiment. Overall, these findings underscore the critical role of metabolic profiling in gaining a deeper understanding of microbial capabilities and addressing the complexities of residue composition and environmental variability.

Background: The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity. Methods: The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h. Results: Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as α-cyclodextrin, D-cellobiose, glycogen, α-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.

Sustainable-forage production is globally increasing, especially in marginal areas where the edaphic conditions for plant growth are not optimal. Soil salinization influences the symbiotic interaction between alfalfa and rhizobia. The efficiency of different symbiotic pairs (Sinorhizobium meliloti—Medicago sativa) was evaluated in relation to NaCl application (100 mM) on two different alfalfa cultivars (Marina and Etrusca) and 21 S. meliloti strains isolated in Algeria. At 100 mM NaCl, it was observed that there was a higher variability of plant dry weight compared to the control. The strains able to improve plant growth at 100 mM NaCl were different and specific for each alfalfa cultivar, highlighting that (symbiont) G × (host) G interaction is magnified under stressed (saline) conditions (E). Three strains were then identified as candidate inoculants for M. sativa cv Marina and used for an in-field experiment with induced stress (no irrigation), together with S. meliloti GR4 (a highly competitive strain). In-field experiments, showed a high variability, and a significant difference of plant biomass was observed only for those inoculated with S. meliloti GR4. Obtained results suggest that multiple traits should be considered for inoculant-strain selection, and for an efficient translation from lab to field, it requires extensive comprehension of the mechanisms driving G × G × E interaction.

Characterisation and evaluation of soil bacteria were conducted in order to select the most potent strains that participate in the degradation of cellulose in unique agroecosystem and climatic conditions. Cellulolytic activity of soil bacteria was estimated using qualitative assays such as growth on selective media followed by screening with Congo red, Gram’s iodine solution, confirmation test on Congo red agar, determination of enzyme production, and sugar utilisation pattern. A total of 159 soil cellulolytic bacterial strains were selected based on shape, size, and colony characteristics. According to the results of all three screening assays, sixty-four, thirty-eight and fifty-one isolates were able to degrade at some level of cellulose, respectively. Partial sequencing of the 16S rRNA gene of 64 bacterial strains obtained using sequences retrieved from the databases indicated the presence of cellulolytic bacteria represented by members of the phyla Actinobacteria (48.44%), followed by Firmicutes (32.81%), Proteobacteria (15.62%) and Bacteroidetes (3.13%). Determination of enzyme production showed that fifteen strains possess endoglucanases activity which ranged from 9.09 to 942.41 nanomoles of MUF (4-methylumbelliferone) mL. Likewise, β-glucosidase enzyme activity was determined in 23.4 % of all isolates. The sugar utilisation pattern of soil bacterial strains displayed the different capabilities of growth and utilisation on various carbon sources, which occur in lignocellulosic materials (cellulose, starch) or their hydrolysates (glucose, galactose, fructose, cellobiose, maltose, lactose, sucrose, trehalose).

Polylactic acid (PLA), a bioplastic synthesized from lactic acid, has a broad range of applications owing to its excellent proprieties such as a high melting point, good mechanical strength, transparency, and ease of fabrication. However, the safe disposal of PLA is an emerging environmental problem: it resists microbial attack in environmental conditions, and the frequency of PLA-degrading microorganisms in soil is very low. To date, a limited number of PLA-degrading bacteria have been isolated, and most are actinomycetes. In this work, a method for the selection of rare actinomycetes with extracellular proteolytic activity was established, and the technique was used to isolate four mesophilic actinomycetes with the ability to degrade emulsified PLA in agar plates. All four strains—designated SO1.1, SO1.2, SNC, and SST—belong to the genus Amycolatopsis. The PLA-degrading capability of the four strains was investigated by testing their ability to assimilate lactic acid, fragment PLA polymers, and deteriorate PLA films. The strain SNC was the best PLA degrader—it was able to assimilate lactic acid, constitutively cleave PLA, and form a thick and widespread biofilm on PLA film. The activity of this strain extensively eroded the polymer, leading to a weight loss of 36% in one month in mesophilic conditions.

Understanding plant–microbe interactions is crucial for improving plants’ productivity and protection. Constraint-based metabolic modeling is one of the possible ways to investigate the bacterial adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. We reconstructed a raw metabolic model of the emerging plant pathogenic bacterium Pectobacterium parmentieri SCC3193 with the use of KBase. The model was curated by using inParanoind and phenotypic data generated with the use of the OmniLog system. Metabolic modeling was performed through COBRApy Toolbox v. 0.10.1. The curated metabolic model of P. parmentieri SCC3193 is highly reliable, as in silico obtained results overlapped up to 91% with experimental data on carbon utilization phenotypes. By mean of flux balance analysis (FBA), we predicted the metabolic adaptation of P. parmentieri SCC3193 to two different ecological niches, relevant for the persistence and plant colonization by this bacterium: soil and the rhizosphere. We performed in silico gene deletions to predict the set of essential core genes for this bacterium to grow in such environments. We anticipate that our metabolic model will be a valuable element for defining a set of metabolic targets to control infection and spreading of this plant pathogen.