Biostimulation effect of different amendments on Cr(VI) recovering microbial community.

The present study used Cr(VI)-polluted microcosms amended with lactate or yeast extract, and nonamended microcosms as control, to investigate how a native bacterial community varied in response to the treatment and during the pollutant removal. Results suggested that providing electron donors resulted in a proliferation of a few bacterial species, with the consequent decrease in observed species richness and evenness, and was a driving force for the bacterial compositional shift. Lactate promoted, in the first instance, the enrichment of fermentative bacteria belonging to Chromobacteriaceae, including Paludibacterium, and Micrococcaceae as observed after 4 days. When the rate of Cr(VI) removal was maximum in microcosms amended with lactate, the most represented taxa were Pseudarcicella and Azospirillum. Using yeast extract as a carbon source and electron donor led instead to the significant enrichment of Shewanella, followed by Vogesella and Acinetobacter on the 4th day, corresponding to 90% of Cr(VI) removed from the system. After the complete Cr(VI) removal, achieved in 7 days in the presence of yeast extract, α-diversity was notably increased. The amendment-specific turnover of the enriched bacterial taxa resulted in a different kinetic of pollutant removal. In particular, yeast extract promoted the quickest Cr(VI) reduction, while lactate supported a slower, but also considerable, pollutant removal from water. Since it is reasonable to assume that a macroscopic effect, such as the observed Cr(VI) removal, involved the overrepresented taxa, deepening the knowledge of the native bacterial community and its changes were used to hypothesize the possible microbial pathways involved.

Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum).

Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter-specific, and inter-ploidy admixture of its genome and lack of in depth genome-wide inheritance and comparative structural studies. Here we describe a new high-quality, phased, chromosome-scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high-density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species. Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr-6 and one of chr-10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter-crossable wild diploid species. These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop.

Enhanced Natural Attenuation of Groundwater Cr(VI) Pollution Using Electron Donors: Yeast Extract vs. Polyhydroxybutyrate.

Remediation interventions based on the native bacteria's capability to reduce Cr(VI) represent a valid strategy in terms of economic and environmental sustainability. In this study, a bioremediation test was carried out using viable microcosms set with groundwater and deep soil (4:1), collected from the saturated zone of an industrial site in Southern Italy that was polluted by ~130 µg L-1 of Cr(VI). Conditions simulating the potential natural attenuation were compared to the enhanced natural attenuation induced by supplying yeast extract or polyhydroxybutyrate. Sterile controls were set up to study the possible Cr(VI) abiotic reduction. No pollution attenuation was detected in the unamended viable reactors, whereas yeast extract provided the complete Cr(VI) removal in 7 days, and polyhydroxybutyrate allowed ~70% pollutant removal after 21 days. The incomplete abiotic removal of Cr(VI) was observed in sterile reactors amended with yeast extract, thus suggesting the essential role of native bacteria in Cr(VI) remediation. This was in accordance with the results of Pearson's coefficient test, which revealed that Cr(VI) removal was positively correlated with microbial proliferation (n = 0.724), and also negatively correlated with pH (n = -0.646), dissolved oxygen (n = -0.828) and nitrate (n = -0.940). The relationships between the Cr(VI) removal and other monitored parameters were investigated by principal component analysis, which explained 76.71% of the total variance.

Chromium Pollution in European Water, Sources, Health Risk, and Remediation Strategies: An Overview.

Chromium is a potentially toxic metal occurring in water and groundwater as a result of natural and anthropogenic sources. Microbial interaction with mafic and ultramafic rocks together with geogenic processes release Cr (VI) in natural environment by chromite oxidation. Moreover, Cr (VI) pollution is largely related to several Cr (VI) industrial applications in the field of energy production, manufacturing of metals and chemicals, and subsequent waste and wastewater management. Chromium discharge in European Union (EU) waters is subjected to nationwide recommendations, which vary depending on the type of industry and receiving water body. Once in water, chromium mainly occurs in two oxidation states Cr (III) and Cr (VI) and related ion forms depending on pH values, redox potential, and presence of natural reducing agents. Public concerns with chromium are primarily related to hexavalent compounds owing to their toxic effects on humans, animals, plants, and microorganisms. Risks for human health range from skin irritation to DNA damages and cancer development, depending on dose, exposure level, and duration. Remediation strategies commonly used for Cr (VI) removal include physico-chemical and biological methods. This work critically presents their advantages and disadvantages, suggesting a site-specific and accurate evaluation for choosing the best available recovering technology.

Enhancement of Chromium (VI) Reduction in Microcosms Amended with Lactate or Yeast Extract: A Laboratory-Scale Study.

A laboratory-scale study was carried out to evaluate the groundwater bioremediation potential of hexavalent chromium (Cr(VI)), taking into account the chromate pollution of an industrial site located in Southern Italy (Apulia Region). The reduction of Cr(VI) was studied on laboratory microcosms, set up in different experimental conditions, namely: ABIO (soil and water sterilized), BIO (soil and water not sterilized), LATT (with the addition of lactate), and YE (with the addition of yeast extract). Control test lines, set up by using sterilized matrices and amendments, were employed to assess the occurrence of the pollutant reduction via chemical processes. By combining molecular (microbial abundance, specific chromate reductase genes (ChR) and the Shewanella oinedensis bacterial strain) with chemical analyses of chromium (VI and III) in the matrices (water and soil) of each microcosm, it was possible to investigate the response of microbial populations to different experimental conditions, and therefore, to assess their bioremediation capability in promoting Cr(VI) reduction. The overall results achieved within this work evidenced the key role of amendments (lactate and yeast extract) in enhancing the biological reduction of hexavalent chromium in the contaminated aqueous phase of laboratory microcosms. The highest value of Cr(VI) removal (99.47%) was obtained in the YE amended microcosms at seven days.

Corrigendum: Can High Throughput Phenotyping Help Food Security in the Mediterranean Area?

[This corrects the article DOI: 10.3389/fpls.2019.00015.].

Can High Throughput Phenotyping Help Food Security in the Mediterranean Area?

According to the IPCC 2014 report the Mediterranean region will be affected by strong climatic changes, both in terms of average temperature and of precipitations regime. This area hosts some half a billion people and the impact on food production will be severe. To implement a climate smart agriculture paradigm and a sustainable increase of agricultural productivity different approaches can be deployed. Agriculture alone consumes 70% of the entire water available on the planet, thus the observed reduction of useful rainfall and growing costs for irrigation water may severely constrain food security. In our work we focused on two typical Mediterranean crops: durum wheat, a rainfed crop, and tomato, an irrigated one. In wheat we explored the possibility of identifying genotypes resilient to water stress for future breeding aims, while in tomato we explored the possibility of using biostimulants to increase the plant capacity of using water. In order to achieve these targets, we used high throughput phenotyping (HTP). Two traits were considered: digital biovolume, a measure based on imaging techniques in the RGB domain, and Water Use Efficiency index as calculated semi-automatically on the basis of evaporation measurements resulting in a high throughput, non-destructive, non-invasive approach, as opposed to destructive and time consuming traditional methods. Our results clearly indicate that HTP is able to discriminate genotypes and biostimulant treatments that allow plants to use soil water more efficiently. In addition, these methods based on RGB quality images can easily be scaled to field phenotyping structure USVs or UAVs.

Durum wheat miRNAs in response to nitrogen starvation at the grain filling stage.

Durum wheat highly depends on nitrogen for seed development and yield, and the obtainment of varieties with a better nitrogen use efficiency is crucial to reduce production costs and environmental pollution. In this study, sequencing of two small RNA libraries obtained from tissues of Ciccio and Svevo cultivars grown under nitrogen starvation conditions produced 84 novel, and 161 conserved miRNAs. Of these, 7 novel and 13 known miRNAs were newly identified in this work. Quantitative PCR analysis of selected miRNAs highlighted that the expression levels of some of them depends on the tissue and on the cultivar, Svevo being the most responsive to nitrogen starvation. A number of target genes were predicted to be involved in nitrogen metabolism. An inverse correlation for the qPCR expression data of miRNA/target pairs miR399b/PHO2, miR393c/AFB2, ttu-novel-61/CCAAT-TF was observed in specific tissues or cultivar. Especially, ttu-novel-61 was down-regulated and its target CCAAT-TF up-regulated in almost all tissues both in Svevo and in Ciccio. Moreover, CCAAT-TF was confirmed to be cleaved by ttu-novel-61 at the expected site. The discovery of miRNAs involved in the response to nitrogen stress represents an important step towards functional analyses, with the final aim to design strategies for improving nitrogen use efficiency in durum wheat.

The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes.

BACKGROUND: The allotetraploid durum wheat [Triticum turgidum subsp. durum (Desf.) Husn.] is a highly economically important species especially in the Mediterranean basin. However, its genomics, transcriptomics and in particular microRNAome are still largely unknown. RESULTS: In the present work, two small RNA libraries from durum wheat Ciccio and Svevo cultivars were generated from different tissues at the late milk (Z77) developmental stage. A total of 167 conserved and 98 potential novel miRNAs were identified in the two libraries and interestingly, three novel miRNAs were found to be derived from ribosomal RNA. Putative target genes were predicted for conserved and novel miRNAs, the majority of which interact with nucleic acids, according to GO terms relative to molecular function. Quantitative qPCR analysis showed that several miRNAs identified were differentially expressed in the mature (Z77) developmental stage compared to young (Z14) tissues. Moreover, target gene expression analysis suggested that in roots, the putative genes encoding for the SQUAMOSA SPL2 and TGA1 proteins are regulated by ttu-miR156n, while MYB3 transcription factor by ttu-miR319f. Additionally, the Photosystem II P680 chlorophyll A apoprotein gene showed an expression level negatively correlated to that of ttu-novel-48 in leaves. CONCLUSION: Our results suggest that, in durum wheat, these genes may play important roles in root/leaf development and are subjected to miRNA regulation. The prediction of novel miRNAs putatively derived from ribosomal RNA opens new perspectives on the study of plant miRNAs.

Development of chloroplast genomic resources for Cynara.

In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.

Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae.

With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the ndhF gene generating an overlap between the ndhF and ycf1 genes. A total of 127 cp simple sequence repeats (cpSSRs) were identified in the artichoke cp genome, potentially suitable for future population studies in the Cynara genus. Parsimony-informative regions were evaluated and allowed to place a Cynara species within the Asteraceae family tree. The eight most informative coding regions were also considered and tested for "specific barcode" purpose in the Asteraceae family. Our results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.

Population structure of Cynara cardunculus complex and the origin of the conspecific crops artichoke and cardoon.

BACKGROUND AND AIMS: Globe artichoke and leafy cardoon, two crops within the same species Cynara cardunculus, are traditionally cultivated in the Mediterranean region and play a significant role in the agricultural economy of this area. The two cultigens have different reproductive systems: artichoke is generally vegetatively propagated, while leafy cardoon is seed propagated. The domestication events underlying the origin of both artichoke and cultivated cardoon from their wild relative and the area of occurrence are not yet fully understood. The aim of this study was to investigate population structure in wild cardoon, globe artichoke and leafy cardoon material and infer domestication events. METHODS: Thirty-five microsatellite (simple sequence repeat) markers, distributed in the C. cardunculus genome, and a large geographical and numerical sampling in southern Europe and North Africa were used to assess population structure and diversity. KEY RESULTS: The results suggest the presence of two distinct domestication events for artichoke and leafy cardoon, and also suggest a new possible scenario, with western wild cardoon having originated from cultivated cardoon escaped from cultivation. Evidence was found for a demographic bottleneck in the past history of globe artichoke. CONCLUSIONS: The results shed new light on the relationships between the three taxa of C. cardunculus and highlight relevant aspects on the evolution of domestication of two crops with a different reproductive system within the same species. It is proposed that the probable centre of origin of artichoke is located in southern Italy, probably Sicily.

Doppler markers of elevated left atrial and ventricular filling pressure in a critically ill patient.

Accurate assessment of intracardiac flows by Doppler echocardiography may add important hemodynamic information in the critically ill patient. Detailed analysis of flow gradients through different sites and their correlation with timing of cardiac events may help us in better understanding the pathophysiology of the underlying disease. We report the clinical case of a 78-year-old patient with septic shock, in whom an A-dip of aortic regurgitation, shortening of diastolic filling, and diastolic mitral regurgitation were detected by Doppler analysis. Pathophysiologic explanation of these phenomena and their evolution after inotropic drug infusion are reported.

Isolation and characterization of novel variants of BBI coding genes from the legume Lathyrus sativus.

A pool of twelve cDNA sequences coding for Bowman-Birk inhibitors (BBIs) was identified in the legume grass pea (Lathyrus sativus L.). The corresponding amino acid sequences showed a canonical first anti-trypsin domain, predicted according to the identity of the determinant residue P(1). A more variable second binding loop was observed allowing to identify three groups based on the identity of residue P(1): two groups (Ls_BBI_1 and Ls_BBI_2) carried a second reactive site specific for chymotrypsin, while a third group (Ls_BBI_3) was predicted to inhibit elastase. A fourth variant carrying an Asp in the P(1) position of the second reactive site was identified only from genomic DNA. A phylogenetic tree constructed using grass pea BBIs with their homologs from other legume species revealed grouping based on taxonomy and on specificity of the reactive sites. Five BBI sequences, representing five different second reactive sites, were heterologously expressed in the yeast Pichia pastoris. The recombinant proteins demonstrated to be active against trypsin, while three of them were also active against chymotrypsin, and one against human leukocyte elastase. Comparative modeling and protein docking were used to further investigate interactions between two grass pea BBI isoforms and their target proteases. Thus two reliable 3D models have been proposed, representing two potential ternary complexes, each constituted of an inhibitor and its target enzymes.

The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis.

BACKGROUND: Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found. Due to low abundance, non conserved miRNAs are difficult to identify and isolate using conventional approaches. Conversely, deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs.No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots. RESULTS: Conserved and novel miRNAs were discovered using accepted criteria. The expression level of selected miRNAs was monitored by quantitative real-time PCR. Targets were predicted and validated for their cleavage site. A total of 122 artichoke miRNAs were identified, 98 (25 families) of which were conserved with other plant species, and 24 were novel. Some miRNAs were differentially expressed according to tissue or condition, magnitude of variation after salt stress being more pronounced in roots. Target function was predicted by comparison to Arabidopsis proteins; the 43 targets (23 for novel miRNAs) identified included transcription factors and other genes, most of which involved in the response to various stresses. An unusual cleaved transcript was detected for miR393 target, transport inhibitor response 1. CONCLUSIONS: The miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.

Cardiac tamponade and bilateral pleural effusion in a very low birth weight infant.

A very low birth weight premature newborn developed a sudden cardiac tamponade due to parenteral fluid extravasation 1 month after central line insertion. Besides tensive pericardial effusion a bilateral pleural effusion also developed. An emergency pericardiocentesis was really life-saving and after pleural fluid removal a complete cardiorespiratory recovery was obtained. Pericardial and bilateral pleural effusions very rarely coexist as a complication of central line extravasation.