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The implementation of organic amendments, such as biochar and compost, can be an effective and innovative environmental friendly option for the recovery of functionality of soils contaminated by potentially toxic elements (PTE). The aim of this study was therefore to assess the influence of a biochar added at 3% w/w (Bio) and its combination with a municipal solid waste compost (MSWC), on the mobility, bioavailability, and phytotoxicity of several (PTE), As (55 mg·kg−1), Sb (84 mg·kg−1), Ni (176 mg·kg−1) and Cr (214 mg·kg−1) present in a contaminated soil (TS). Sequential extraction procedures showed that biochar and its combination with MSWC decreased soil labile PTE, with biochar increasing remarkably their residual fraction compared to TS-soil (+47, 59, 4, and 9% for As, Sb, Cr, and Ni respectively). Amendment addition also favored an increase of the metabolic potential and catabolic versatility of soil microbial communities, as well as soil functionality. Dehydrogenase, β-glucosidase, and urease activities in TS+Bio showed a significant increase (+45, 16, and 21% respectively) with respect to control. Results from a pot experiment showed that all treatments increased the plant yields significantly in the order: Bio>Bio-MSWC>TS (e.g. the shoot length of green bell pepper and wheat grown on Bio increased, respectively, by a factor of 1.8 and 1.2 compared to TS plants). The amendments addition also reduced PTE transfer from root to shoot. Overall, the results obtained indicated that biochar addition at 3% can be an effective environmental friendly strategy for the in situ stabilization of PTE in polluted soils.

The suitability for aided phytoremediation of Cynara cardunculus L. var. altilis and municipal solid waste compost (MSWC) applied at 2% and 4 % rates was evaluated in a multi potentially toxic element (PTE)-contaminated mining soil (Pb ~ 15,383 mg kg−1, Zn ~ 4076 mg kg−1, As ~ 49 mg kg−1, Cd ~ 67 mg kg−1, Cu ~ 181 mg kg−1, and Sb ~ 109 mg kg−1). The growth of C. cardunculus significantly increased with compost amendment and followed the order: MSWC-4% > MSWC-2% > Control. PTE concentrations in the roots of plants grown on amended soils decreased compared with control plants (i.e., less than ~ 82, 94, and 88% for Pb, Zn, and Cd respectively). PTE translocation from roots to shoots depended on both PTE and amendment rate but values were generally low (i.e., < 1). However, PTE mineralomasses were always higher for plants grown on MSWC-amended soils because of their higher biomass production, which favored an overall PTE bioaccumulation in roots and shoots. After plant growth, labile As and Sb increased in amended soils, while labile Pb, Zn, Cu, and Cd significantly decreased. Likewise, dehydrogenase and urease activities increased significantly in planted soils amended with MSWC. Also, the potential metabolic activity and the catabolic versatility of soil microbial communities significantly increased in planted soils amended with MSWC. Overall, our results indicate that C. cardunculus and MSWC can be effective resources for the aided phytoremediation of multi PTE-contaminated soils.

In this study, the effectiveness of softwood-derived biochar (BC) in the retention of potentially toxic elements (PTE, i.e., Cu(II), Pb(II), As(V), and Sb(V)) was evaluated at different pH values (4.5, 6.0, and 7.0), along with its capacity to alleviate PTE phytotoxicity. At all pH values, sorption and kinetic isotherms followed the trend: Pb(II) (e.g., ~ 0.56 mmol g−1at pH 6.0) > Cu(II) (e.g., ~ 0.33 mmol g−1at pH 6.0) > As(V) (e.g., ~ 0.29 mmol g−1at pH 6.0) > Sb(V) (e.g. ~ 0.24 mmol g−1at pH 6.0). Kinetic data strongly correlated with the pseudo-second-order kinetic equation; Langmuir and Freundlich isotherm models suggested monolayer sorption of Cu(II), Pb(II), and As(V) onto the BC surface and the interaction of Sb(V) with BC sites characterized by distinct sorption energy (i.e., multilayer sorption). Scanning electron microscopy (SEM) with energy-dispersive X-ray (EDX) analysis of PTE-saturated BC showed that Pb(II) was mainly associated with O, Sb(V) with Ca and Fe, while Cu(II) and As(V) with Fe and O. This suggested that hydroxyl and carboxyl functional groups, amorphous Fe oxy-hydroxides, as well as PTE precipitation with BC components were likely responsible for BC sorption capacity. Treatment of PTE-saturated BC with Ca(NO3)2and a range of environmentally relevant organic acids indicated that 6–11% of PTE were loosely bound and easily exchangeable, while up to 60% could be mobilized by the organic acids. Hydroponic plant-growth experiments using triticale plants showed that BC stimulated plant growth in the presence of PTE and reduced their phytotoxicity.

Organic based amendments can be used to reduce metal(loid)s mobility in polluted soils and alleviate possible toxicity phenomena towards soil microbiota. Therefore, the objectives of this study were to evaluate the influence of municipal solid waste compost (MSWC) on the mobility of metal(loid)s in different contaminated soils and to determine the amendment effect on selected soil biochemical and microbial features. To this aim, MSWC was added at two rates (1 and 3% w/w) to different soils sampled in distinct regions of Lebanon (Halba and Terbol, i.e. HS and TS respectively) polluted with metal(loid)s such as As (total concentrations between 31 and 54 mg·kg−1) and Sb (between 93 and 120 mg·kg−1), and trace metals such as Ni, Cr and Zn. After two months of soil-amendment contact, compost addition at both rates significantly increased the non-extractable fractions of As, Sb, Ni, Cr and Zn (e.g. +25% of residual Sb in TS-MSWC 3% with respect to untreated TS), while decreased the environmentally-relevant water soluble and exchangeable fractions of all the metal(loid)s. This effect was more relevant for both soils when 3% MSWC was applied. The amendment addition similarly affected the community level physiological profile (Biolog CLPP) of the respective soil culturable microbial communities, which however showed an opposite trend in the two soils. In particular, compost addition increased the metabolic potential and catabolic versatility of the HS microbial community (compared to the untreated control), while the same proxies were significantly reduced in the amended TS soil. Differently, soil dehydrogenase (DHG), β-glucosidase (β-GLU) and urease (URE) activities were significantly enhanced in both soils treated with compost (e.g. + 17, 45 and 27% for DHG, URE and β-GLU in TS-MSWC 3% with respect to untreated TS). The results obtained showed that the addition of MSWC, particularly at the 3% rate, was effective at fixing the metal(loid)s present in both soils, had a substantial influence on the structure of the soil microbial communities and a positive effect on soil functionality. Taken together the results presented suggest that MSWC can be used as an alternative and environmental friendly amendment for the in situ remediation of metal(loid)s-polluted soils.

Soil microbial communities (SMCs) are important drivers of forest ecosystem functions and services. To optimize afforestation practices, it is important to understand how pure and mixed plantations can affect SMCs and their functioning. Therefore, the objective of this work was to investigate the SMC structure and function of six Mediterranean woody species grown as monocultures, and of six selected 1:1 combinations. SMC structure was assessed through the abundance estimation of different culturable heterotrophic microbial populations (i.e. bacteria, fungi, actinomycetes, Pseudomoas spp. and aerobic spore-forming bacteria) and the Biolog community level physiological profile, while soil biochemical functioning was estimated by quantifying soil dehydrogenase (DHG) activity. Species richness (SR) did not increase the abundance of culturable heterotrophic microbial populations, nor the number of carbon sources metabolized by the microbial communities (Biolog richness) or DHG activity. However, SR significantly decreased the potential metabolic activity (Biolog AWCD) of soil microbial populations. Leaf type significantly affected soil microbial and biochemical features, particularly for monocultures where conifer plots were characterized by a significantly higher fungal/bacterial ratio, reduced AWCD and richness as well as reduced DHG values. Significant interactions between tree species in mixed plots were noticed as well as significant correlations between plant community weighted mean (CWM) traits and soil microbial and biochemical features. Both SMC structure and function were clearly influenced by tree plantations and, importantly, microbial populations of monocultures and mixed plantations, and their functioning, were governed by different CWM traits.

This study aimed to evaluate the influence of Eisenia fetida (Savigny), added to an acidic soil contaminated with potentially toxic elements (PTEs; As, Sb, Cd, Pb, Zn) and amended with a softwood-derived biochar (2 and 5% w/w), on the mobility of PTEs and soil health (i.e. nutrient availability, enzyme activity and soil basal respiration). The PTEs bioaccumulation by E. fetida and the acute ecotoxicity effects of the amended soils were also evaluated. The interaction between earthworms and biochar led to a significant increase in soil pH, organic matter, dissolved organic carbon content, cation exchange capacity, and exchangeable Ca compared to the untreated soil. Moreover, the water-soluble and readily exchangeable PTE fraction decreased (with the exception of Sb) between 1.2- and 3.0-fold in the presence of biochar and earthworms. Earthworms, biochar, and their combination, led to a reduction of phosphomonoesterase activity which in soils amended with biochar and earthworms decreased between 2.2- and 2.5-fold with respect to the untreated soil. On the other hand, biochar and earthworms also enhanced soil basal respiration and protease activity. Although the survival rate and the weight loss of E. fetida did not change significantly with the addition of 2% biochar, adding the highest biochar percentage (5%) resulted in a survival rate that was ~2-fold lower and a weight loss that was 2.5-fold higher than the other treatments. The PTE bioaccumulation factors for E. fetida, which were less than 1 for all elements (except Cd), followed the order Cd > As>Zn > Cu > Pb > Sb and were further decreased by biochar addition. Overall, these results highlight that E. fetida and biochar, especially at 2% rate, could be used for the restoration of soil functionality in PTE-polluted environments, reducing at the same time the environmental risks posed by PTEs, at least in the short time.

Background The crescent availability of high-resolution cardiac imaging allows detection of myocardial structural variations. Differentiate these entities from others with different clinical significance can be challenging. Clinicians should be familiar with myocardial clefts to avoid erroneous diagnosis. Case summary A 63-year-old smoker man alerted the emergency medical system for sudden chest pain. The electrocardiogram showed Pardee wave in inferior leads. Coronary angiography evidenced a 100% occlusion of right coronary artery that was treated by angioplasty and drug-eluting stent implantation with optimal angiographic result. At ventriculography, two fissure-like protrusion were observed in the inferior wall. Urgent transthoracic echocardiogram (TTE) demonstrated two deep fissures on the mid-inferior wall, contained by a thin sub-epicardial layer, with sub-total obliteration during systole. A diagnosis of myocardial clefts was suspected and after Heart Team discussion, a conservative strategy was proposed. Early cardiac magnetic resonance (CMR) confirmed two myocardial crypts on the mid-inferior wall. Stability of myocardial fissures and absence of left ventricular remodelling was confirmed by TTE, in a 2 years of follow-up period. Discussion Myocardial cleft should always be considered in the differential diagnosis of myocardial wall defects. In a patient presenting with an acute myocardial infarction, the main differential diagnosis is pseudoaneurysm. In this setting modified TTE views and meticulous analysis of CMR sequences are recommended to confirm the diagnosis and estimate the risk of myocardial rupture.

The effect of long-term ageing (up to 700 days) on the mobility, potential bioavailability and bioaccessibility of antimony (Sb) was investigated in two soils (S1: pH 8.2; S2: pH 4.9) spiked with two Sb concentrations (100 and 1000 mg·kg−1). The Sb mobility decreased with ageing as highlighted by sequential extraction, while its residual fraction significantly increased. The concentration of Sb (CDGT), as determined by diffusive gradients in thin films (DGT), showed a reduction in potential contaminant bioavailability during ageing. The DGT analysis also showed that Sb-CDGT after 700 days ageing was significantly higher in S1–1000 compared to S2–1000, suggesting soil pH plays a key role in Sb potential bioavailability. In-vitro tests also revealed that Sb bioaccessibility (and Hazard Quotient) decreased over time. Linear combination fitting of Sb K-edge XANES derivative spectra showed, as a general trend, an increase in Sb(V) sorption to inorganic oxides with ageing as well as Sb(V) bound to organic matter (e.g. up to 27 and 37% respectively for S2–100). The results indicated that ageing can alleviate Sb ecotoxicity in soil and that the effectiveness of such processes can be increased at acidic pH. However, substantial risks due to Sb mobility, potential bioavailability and bioaccessibility remained in contaminated soils even after 700 days ageing. Refereed/Peer-reviewed

In the context of the coronavirus disease 2019 pandemic, myocardial injury is a relatively frequent finding. Progression to cardiogenic shock has been rarely described, especially in healthy young patients. The underlying mechanisms are to date controversial. A previously healthy 18‐year‐old female teenager affected by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) developed fulminant cardiogenic shock requiring a prompt extracorporeal membrane oxygenation support. Cardiac involvement was predominant compared with the pulmonary one. Myocardial biopsies were performed; and in order to clarify the pathophysiology of the acute heart failure, optical and transmission electron microscopy study was realized. Two additional immunohistology techniques were developed in order to (i) detect a SARS‐CoV‐2 recombinant fusion nucleoprotein by using a specific antibody and (ii) study fractalkine expression induced by activated endothelium because this molecule is well known to be elevated in patients with severe cytokine release syndrome. SARS‐CoV‐2 genome was not detected in the myocardium. Even if the clinical presentation, laboratory markers, and cardiac imaging techniques strongly suggested fulminant myocarditis, histology and immunohistology were not fully consistent with this diagnosis according to the Dallas criteria. Although rare suspected coronavirus particles were found by transmission electron microscopy in the cardiac endothelium, neither significant immunoreactivity for the viral nucleocapsid protein nor image suggestive of endotheliitis was detected. Intense endothelial immunoreactivity pattern for fractalkine expression was observed. From a clinical point of view, the left ventricular systolic function gradually improved, and the patient survived after a long stay in the intensive care unit. Our observations suggest that a massive cytokine storm induced by SARS‐CoV‐2 infection was the main cause of the cardiogenic shock, making a direct viral injury pathway very unlikely.

Antimony (Sb) and its compounds are emerging priority pollutants which pose a serious threat to the environment. The aim of this study was to evaluate the short-term fate of antimonate added to different soils (S1 and S2) with respect to its mobility and impact on soil microbial communities and soil biochemical functioning. To this end, S1 (sandy clay loam, pH 8.2) and S2 (loamy coarse sand, pH 4.9) soils were spiked with 100 and 1000 mg Sb(V) kg−1 soil and left in contact for three months. Sequential extractions carried out after this contact time indicated a higher percentage of labile antimony in the Sb-spiked S1 soils than S2 (e.g. ~13 and 4% in S1 and S2 treated with 1000 mg Sb(V) kg−1 respectively), while the opposite was found for residual (hardly bioavailable) Sb. Also, a reduced number of culturable heterotrophic bacteria was recorded in Sb-spiked S1 soil (compared to the unpolluted S1), while an increased one was found in S2. Heterotrophic fungi followed the opposite trend. Actinomycetes and heat-resistant aerobic bacterial spores showed a variable trend depending on the soil type and Sb(V) treatment. The Biolog community level physiological profile indicated a reduced metabolic activity potential of microbial communities from the Sb-spiked S1 soils (e.g. 2-fold for Sb-1000). The soil dehydrogenase activity followed the same trend. High-throughput 16S rRNA amplicon sequencing analysis revealed that Sb did not influence the bacterial α-diversity in both soils, while significantly affected the composition of the respective soil bacterial communities. Several phyla (e.g. Nitrosospira Nitrososphaeraceae, Adheribacter) were found positively correlated with the concentration of water-soluble Sb in soil. Overall, the results obtained suggest that the risk assessment in soils polluted with antimony should be a priority especially for alkaline soils where the high mobility of the anionic Sb(OH)6ˉ species can pose, at least in the short-term, a serious threat for soil microbial abundance, diversity and functionality, soil fertility and eventually human health. Refereed/Peer-reviewed

Assisted phytoremediation, i.e. the combination of amendment and plant cultivation to remove potentially toxic elements (PTE) from soil, or to reduce their mobility and toxicity, can represent an effective gentle remediation option for the recovery of PTE-contaminated soils. The aim of this study was to evaluate the suitability of different grass and legume species, such as Arundo donax L., Hordeum vulgare L. and Lupinus albus L., in assisted phytoremediation programs of PTE-contaminated soils in combination with a municipal solid waste compost (MSWC) used at 2 and 4% rates. The soil was heavily contaminated by different PTE, i.e. Pb (15,383 mg kg − 1 ), Zn (4,076 mg kg − 1 ), Sb (109 mg kg − 1 ), Cd (67 mg kg − 1 ) and As (49 mg kg − 1 ). The selected plant species were able to grow in the contaminated soil, and their biomass production was significantly influenced by the compost either positively (e.g. A. donax) or negatively (e.g. H. vulgare roots). Compost addition significantly decreased or did not influence the PTE uptake and bioaccumulation factors of A. donax and H. vulgare roots and shoots, while it increased those of L. albus (particularly in roots) with respect to As, Sb, Pb and Cu. Finally, MSWC increased the PTE removal efficiency of A. donax (and partially of L. albus but not by H. vulgare), i.e. its ability to bioaccumulate PTE in the below ground organs, especially when grown in soils amended with 4% MSWC. The results indicated that A. donax, and in selected cases L. albus, can be used in combination with MSWC for the phytostabilization of PTE-contaminated soils.

In this study we evaluated the microbiological and biochemical impact of iron-based water treatment residuals (Fe-WTRs) and municipal solid waste compost (MSWC), alone and combined, on three different soils co-contaminated with arsenic (As) and trace-metals (TM), i.e. Pb, Cu and Zn. Overall, all the amendments considered significantly increased the abundance of culturable heterotrophic bacteria, with MSWC showing the greatest impact across all soils (up to a 24% increase). In most of treated soils this was accompanied by a significant reduction of both the (culturable) fungal/bacterial ratio, and the proportion of culturable As(V)- and As(III)-resistant bacteria with respect to total bacterial population. The catabolic potential and versatility of the resident microbial communities (assessed by community level physiological profile) was highly soil-dependent and substantial increases of both parameters were observed in the amended soils with the higher total As concentration (from approx. 749 to 22,600 mg kg−1). Moreover, both carbon source utilisation profile and 16S rRNA soil metagenome sequencing indicated a significant impact of MSWC and Fe-WTRs on the structure and diversity of soil microbial communities, with Proteobacteria, Actinobacteria and Firmicutes being the most affected taxa. The assessment of selected soil enzyme activities (dehydrogenase, urease and β-glucosidase) indicated an increase of metabolic functioning especially in soils treated with MSWC (e.g. dehydrogenase activity increased up to 19.5-fold in the most contaminated soil treated with MSWC). Finally, the microbial and biochemical features of treated (and untreated) contaminated soils (i.e. total bacterial counts, catabolic potential and versatility and soil enzyme activities) were highly correlated with the concentrations of labile As and TM in these latter soils and supported a clear role of the tested amendments (especially MSWC) as As- and TM-immobilising agents.

In this study, we investigated the cooperative effect of caffeic (CAF) and malic (MAL) acids as well as the role of polygalacturonic acid (PGA) on the toxicity of copper (Cu)(II) towards triticale plants (× Triticosecale Wittm.). Plant growth experiments carried out in hydroponic solutions at pH 6.0 revealed that CAF and PGA, but not MAL, were quite effective at reducing Cu(II) phytotoxicity and that MAL addition abolished the positive effects of CAF. The study of the CAF-Cu(II) system in aqueous solution clearly indicated that the lower toxicity of Cu(II) in the presence of CAF was due to the occurrence of a redox reaction between CAF and Cu(II), while the phytotoxicity recorded in the Cu(II)-CAF-MAL system was attributed to a competitive effect of MAL in the Cu(II) complexation by CAF, which ultimately reduced the redox activity. The lowest Cu(II) phytotoxicity recorded in the presence of PGA was attributed to the high affinity of the polysaccharidic matrix towards the metal ion. The results from this study shed new light on the Cu(II)-detoxifying action of selected root exudates and highlight the negative cooperation of MAL on the Cu(II)-detoxifying activity by CAF.

Four iron and aluminium-based products, including red mud (RM), hematite (Fe 2 O 3 ), an iron-rich water treatment residual (Fe-WTR) and amorphous Al hydroxide (Al-OH), were evaluated for their effectiveness at stabilising As and heavy metals (i.e. Cd, Cu, Pb, Zn) in a circumneutral contaminated soil [As (2105 mg kg −1 ), Cd (18 mg kg −1 ), Cu (264 mg kg −1 ), Pb (710 mg kg −1 ), Zn (522 mg kg −1 )]. Treatment impacts on soil microbial and biochemical features (i.e. microbial biomass-C, microbial counts, 16S rRNA PCR-TTGE of culturable bacteria, dehydrogenase, urease and β-glucosidase activity, Biolog derived parameters-AWCD and richness) as well as bean ( Phaseolus vulgaris ) and wheat ( Triticum vulgare ) growth were also assessed. After 6 months equilibration, all the amendments (application rate 3% w/w) but RM reduced labile As while only Al-OH reduced the concentration of water-soluble heavy metals. Despite the highest bioavailability of contaminants, most of the soil microbial and biochemical features monitored (i.e. microbial biomass-C, total bacterial counts, dehydrogenase activity and AWCD) were significantly higher in the RM-soil. Bean germination was completely inhibited in RM-soil while wheat growth was similar to that of the control. The Al-OH treatment was best overall, promoting microbial abundance, diversity and activity while increasing bean and wheat growth and reducing As accumulated in plant shoots. Results suggest that Al-OH is a suitable candidate for field evaluations while the use of RM in the remediation of circumneutral or subalkaline contaminated soils should be reconsidered.

Two strains of Gram-stain-negative, rod-shaped bacteria were isolated from root nodules of the South African legume Rhynchosia ferulifolia and authenticated on this host. Based on phylogenetic analysis of the 16S rRNA gene, strains WSM3930 and WSM3937T belonged to the genus Burkholderia , with the highest degree of sequence similarity to Burkholderia terricola (98.84 %). Additionally, the housekeeping genes gyrB and recA were analysed since 16S rRNA gene sequences are highly similar between closely related species of the genus Burkholderia . The results obtained for both housekeeping genes, gyrB and recA, showed the highest degree of sequence similarity of the novel strains towards Burkholderia caledonica LMG 19076T (94.2 % and 94.5 %, respectively). Chemotaxonomic data, including fatty acid profiles and respiratory quinone data supported the assignment of strains WSM3930 and WSM3937T to the genus Burkholderia . DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains WSM3930 and WSM3937T from the most closely related species of the genus Burkholderia with validly published names. We conclude, therefore, that these strains represent a novel species for which the name Burkholderia rhynchosiae sp. nov. is proposed, with strain WSM3937T ( = LMG 27174T = HAMBI 3354T) as the type strain.

Changes of pasture communities consequent to management practices resulting from land abandonment considerably affect the structure and function of the ecosystem. This study analyses the consequences of grazing abandonment in terms of plant and soil microbial diversity and fertility, on a Mediterranean upland sheep pasture, over a short period (five years). Grazing was experimentally excluded by fencing ten 10×10 m permanent plots within an area that had supported grazing until 2000, by 0.23 sheep ha−1. Plant and soil microbial communities and physicochemical parameters were monitored within the fenced and unfenced control plots, during three sampling times from 2000 (before the fencing) to 2005. Grazing cessation notably altered the floral composition, with an average dissimilarity of 96.7% between the vegetation communities, over five years. No significant change occurred in the control plots that were grazed throughout the sampling period. This work highlighted that, over a short term, the structural change in the specific plant composition affected only the grass species, confirming that grazing favours the small-sized species over the annual species. Further, it was evident that species groups of conservational and phytogeographic interest, like the endemic and Mediterranean-Atlantic species, tended to disappear with pasture abandonment and were substituted by more widespread species throughout the Mediterranean or even the world. Pasture abandonment was accompanied by an increase of soil pH and a decrease in soil organic matter and soil nitrogen. The microbial parameters recorded at three different sampling times revealed a substantial effect of the plant community, or the time of grazing abandonment, on soil microbial abundance and diversity. Considerable importance is given to the consequences of pasture abandonment on the conservation of plant and microbial diversity and on soil fertility.

In this study we report on the interactions between the water-soluble fraction (WSF) of two municipal solid waste composts (C1- and C2-WSF) with Pb(II) and Cu(II) ions at pH 4.5. The Me(II) addition to the compost-WSFs led to the formation of soluble Me(II)-organic complexes (as highlighted by FT-IR spectroscopy), and to a decrease of the trace metals' solubility, which was greater for Pb(II) than Cu(II). This was due to the formation of insoluble Me(II) complexes involving the water-soluble organic carbon (WSOC) and the inorganic anions within both WSFs [1.10 and 0.62 mmol L−1 and 2.06 and 0.42 mmol L−1 of Pb(II) and Cu(II) precipitated from C1- and C2-WSF respectively, when 6.4 mmol L−1 Me(II) was added]. A loss of WSOC from both WSFs, i.e. ∼13% and

Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering Sassari, Sardinia in 1995. WSM1592 is highly effective at fixing nitrogen with H. coronarium, and is currently the commercial Sulla inoculant strain in Australia. Here we describe the features of R. sullae strain WSM1592, together with genome sequence information and its annotation. The 7,530,820 bp high-quality permanent draft genome is arranged into 118 scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes. This rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. Electronic supplementary material The online version of this article (doi:10.1186/s40793-015-0020-2) contains supplementary material, which is available to authorized users.

Sinorhizobium medicae WR101 was identified as a mutant of WSM419 that contained a minitransposon-induced transcriptional gusA fusion activated at least 20-fold at pH 5.7. The expression of this fusion in moderately acid conditions was dependent on the calcium concentration; increasing the calcium concentration to enhance cell growth and survival in acid conditions decreased the expression of the fusion. A gene region containing the gusA fusion was sequenced, revealing five S. medicae genes: tcsA, tcrA, fsrR, lpiA and acvB. The gusA reporter in WR101 was fused to lpiA, which encodes a putative transmembrane protein also found in other Alphaproteobacteria such as Sinorhizobium meliloti, Rhizobium tropici and Agrobacterium tumefaciens. As LpiA has partial sequence similarity to the lysyl-phosphatidylglycerol (LPG) synthetase FmtC/MprF from Staphylococcus aureus, membrane lipid compositions of S. medicae strains were analysed. Cells cultured under neutral or acidic growth conditions did not induce any detectable LPG and therefore this lipid cannot be a major constituent of S. medicae membranes. Expression studies in S. medicae localized the acid-activated lpiA promoter within a 372 bp region upstream of the start codon. The acid-activated transcription of lpiA required the fused sensor–regulator product of the fsrR gene, because expression of lpiA was severely reduced in an S. medicae fsrR mutant. S. meliloti strain 1021 does not contain fsrR and acid-activated expression of the lpiA-gusA fusion did not occur in this species. Although acid-activated lpiA transcription was not required for cell growth, its expression was crucial in enhancing the viability of cells subsequently exposed to lethal acid (pH 4.5) conditions.

Bacillus thuringiensis is a Gram positive bacterium that is used for the production of biopesticides. The toxic action of different strains and serovars ofB. thuringiensis can be extremely selective towards specific pests, or, in contrast, it can affect a wide variety of non-target organisms such as insects, vertebrates or humans. A reliable characterization of the cultivated strains is of primary importance for the biopesticide industry, in order to assess the contamination of the final product with strains with different pesticide actions or that might be dangerous for human health. The aim of this study was to develop useful methods for the typing of differentB. thuringiensis strains using two PCR-based methods, RAPD and Rep-PCR with BOXA1R and ERIC2 primers. The molecular fingerprints obtained using ERIC2-PCR showed a reliable ability to discriminateBacillus thuringiensis strains.

Nitrogen fixing rhizobia associated with the Medicago L. genus belong to two closely related species Sinorhizobium medicae and S. meliloti. To investigate the symbiotic requirements of different Medicago species for the two microsymbionts, 39 bacterial isolates from nodules of eleven Medicago species growing in their natural habitats in the Mediterranean basin plus six historical Australian commercial inocula were symbiotically characterized with Medicago hosts. The bacterial species allocation was first assigned on the basis of symbiotic proficiency with M. polymorpha. PCR primers specific for 16S rDNA were then designed to distinguish S. medicae and S. meliloti. PCR amplification results confirmed the species allocation acquired in the glasshouse. PCR fingerprints generated from ERIC, BOXA1R and nif-directed RPO1 primers revealed that the Mediterranean strains were genetically heterogenous. Moreover PCR fingerprints with ERIC and BOX primers showed that these repetitive DNA elements were specifically distributed and conserved in S. meliloti and S. medicae, clustering the strains into two divergent groups according to their species. Linking the Sinorhizobium species with the plant species of origin we have found that S. medicae was mostly associated with medics well adapted to moderately acid soils such as M. polymorpha, M. arabica and M. murex whereas S. meliloti was predominantly isolated from plants naturally growing on alkaline or neutral pH soils such as M. littoralis and M. tornata. Moreover in glasshouse experiments the S. medicae strains were able to induce well-developed nodules on M. murex whilst S. meliloti was not infective on this species. This feature provides a very distinguishing characteristic for S. medicae. Results from the symbiotic, genotypic and cultural characterization suggest that S. meliloti and S. medicae have adapted to different Medicago species according to the niches these medics usually occupy in their natural habitats.

Ensifer medicae Di28 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago spp. Di28 was isolated in 1998 from a nodule recovered from the roots of M. polymorpha growing in the south east of Sardinia (Italy). Di28 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. murex and is capable of establishing a partially effective symbiotic association with the perennial M. sativa. Here we describe the features of E. medicae Di28, together with genome sequence information and its annotation. The 6,553,624 bp standard draft genome is arranged into 104 scaffolds of 104 contigs containing 6,394 protein-coding genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

In this study we evaluated the influence of ground purple sea urchin (Paracentrotus lividus) endoskeletons, a processing waste common to all edible sea urchin plants, on the chemical, biochemical and microbiological features of an acidic (pH 5.65) sandy-loam soil. The purple sea urchin endoskeletons were characterized by a high content of total carbonates (∼94%), a moderately alkaline pH in water (pH 7.88) and electrical conductivity values (3.55 mS/cm) very similar to those of commercial lime. To evaluate the influence of the P. lividus endoskeletons on soil properties four different amendment rates were tested, notably 0.5, 1.0, 3.0 and 5.0% based on soil dry weight, and the effects compared with those recorded on unamended control soil. The addition of the purple sea urchin processing waste caused an immediate and significant pH increase which was positively related to the rate of the amendment addition. After a six months equilibration period, the differences in soil pH were still evident and significant increases of electrical conductivity and available phosphorus were also detected in soils with the higher amendment rates. The number of heterotrophic and cellulolytic bacteria and actinomycetes significantly increased after amendment addition while the number of culturable fungi steadily declined. The analysis of the Biolog Community Level Physiological Profile indicated a clear influence of the purple sea urchin processing waste on the structure of the native microbial community while a significant increase of microbial functionality (i.e. dehydrogenase activity) was recorded in soil treated with the higher amendment rates (i.e. 3.0 and 5.0%). The improvement of microbial abundance and functionality as well as the change of the microbial community structure were ascribed to the pH shift induced by the P. lividus processing waste. To investigate possible effects on soil fertility, dwarf bean (Phaseolus vulgaris) and wheat (Triticum vulgare) growth were also assessed in a pot experiment. Plant growth was unaffected (wheat) or stimulated (bean) by the amendment addition in the 0.5-3.0% range while the higher amendment rate (i.e. 5.0%) was detrimental for both plant species indicating a phytotoxic effect which could be due to different factors such as an excess of calcium in soil, a suppression of Mg uptake or the higher EC values detected at the highest amendment rate. It is concluded that ground P. lividus endoskeletons have potential as a soil amendment to ameliorate chemical and biological properties of acidic Mediterranean soils. This seems particularly relevant, especially at the lower amendment rates, since for the first time, a sustainable management system is proposed for P. lividus processing waste, which foresees economic value in the sea urchin by-product through its re-use within the agricultural production system.

In this study we investigated the sorption of sulfamethazine (SMZ) in two soils with different physico-chemical properties and the sulfonamide short-term influence on the microbial community structure and function. The presence of manure increased the SMZ sorption, the uppermost level being measured on soil with the lower pH and the higher manure content allowed by the Italian regulation. The sulfonamide desorption was hysteretic on both soils. SMZ addition to soil at the concentration of 53.6 μg/g had a significant short-term negative impact on readily culturable bacteria, potential metabolic activity (Biolog CLPP) and soil enzyme activity. Moreover, a shift of the culturable microbial populations towards a lower bacteria/fungi ratio was observed after SMZ addition. Despite the observed SMZ effects disappeared almost completely after 7 day, structural changes of microbial communities were still present in SMZ-treated soils. The results presented are remarkable since previous studies addressing the SMZ impact on soil microbial parameters failed to highlight any significant effect of the sulfonamide on microbial abundance and diversity.

Diet plays a major role in modulating the fatty acid composition of ruminant milk. It is also well known that the intake of fresh forages has a positive influence on polyunsaturated fatty acid (PUFA), particularly CLA and omega- 3, compared with diets based on dry forage and concentrates. Altitude influences, directly, grass availability and botanical composition of the pasture, and, indirectly, the amount of concentrate supplemented to the diet. Therefore, the altitude where farms are located at may give indirect information about the type of feeding system trough analysis of milk fat. The objective of this survey was to investigate variations in the milk fatty acid profile, focusing on the content of vaccenic acid (VA), conjugated linoleic acid (CLA) and n-3 fatty acid (FA), of Sarda dairy ewes flocks located at different altitudes throughout Sardinia. Bulk milk samples were collected in spring (April) and in summer (July) from 36 flocks located at different altitudes: 3 flocks in the lowlands (Low), 3 flocks in the hills (Hill) and 3 in the highlands (High) in 4 provinces (Sassari, Nuoro, Oristano and Cagliari) of Sardinia (Italy). Milk fatty acid profile was analyzed by gas-chromatography. Data were analyzed with a linear model with altitude (A), season (S), province (P) and altitude x season as fixed factors. The interaction was never significant. The season influenced significantly almost all fatty acids analyzed. The proportion of short chain FA (C4-C10) decrease (10.0 vs 7.0 mg/100 mg FA; Pcis9) increased significantly from spring to summer (22.3 vs 25.1 mg/100 mg FA; Ptrans-11 18:1) that decrease from 1.6 vs 0.8 mg/100 mg FA. No variation in cis9, trans11 CLA has been observed between spring and summer (1.0 vs 0.8 mg/100 mg FA). A reduction of PUFA (5.64 vs 5.10; P

The microbial ecology of cork oak rhizosphere was investigated using the Biolog community level physiological profile (CLPP) that provides a unique metabolic fingerprint helpful for the characterization of complex microbial communities. Microbial populations from the rhizosphere of cork oak plants growing at three different sites within the same area were characterized using CLPP and compared. The sites were distinguished by a different soil management under the tree cover and, in general terms, by a different anthropogenic impact. The comparison of metabolic fingerprints of the different microbial populations showed the existence of a relationship between general microbial activity and functional biodiversity in the rhizosphere and the level of anthropogenic impact. Particularly the presence of grazing animals, soil tillage and fire could be identified as the main factors affecting both the general microbial activity and the structure of microbial populations from cork oak rhizospheres.

Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369, together with genome sequence information and its annotation. The 6,402,557 bp standard draft genome is arranged into 307 scaffolds of 307 contigs containing 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.