Unraveling the plant diversity of the Amazonian canga through DNA barcoding.

The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.

Mapping and quantification of ferruginous outcrop savannas in the Brazilian Amazon: A challenge for biodiversity conservation.

The eastern Brazilian Amazon contains many isolated ferruginous savanna ecosystem patches (locally known as 'canga vegetation') located on ironstone rocky outcrops on the top of plateaus and ridges, surrounded by tropical rainforests. In the Carajás Mineral Province (CMP), these outcrops contain large iron ore reserves that have been exploited by opencast mining since the 1980s. The canga vegetation is particularly impacted by mining, since the iron ores that occur are associated with this type of vegetation and currently, little is known regarding the extent of canga vegetation patches before mining activities began. This information is important for quantifying the impact of mining, in addition to helping plan conservation programmes. Here, land cover changes of the Canga area in the CMP are evaluated by estimating the pre-mining area of canga patches and comparing it to the actual extent of canga patches. We mapped canga vegetation using geographic object-based image analysis (GEOBIA) from 1973 Landsat-1 MSS, 1984 and 2001 Landsat-5 TM, and 2016 Landsat-8 OLI images, and found that canga vegetation originally occupied an area of 144.2 km2 before mining exploitation. By 2016, 19.6% of the canga area was lost in the CMP due to conversion to other land-use types (mining areas, pasturelands). In the Carajás National Forest (CNF), located within the CMP, the original canga vegetation covered 105.2 km2 (2.55% of the CNF total area), and in 2016, canga vegetation occupied an area of 77.2 km2 (1.87%). Therefore, after more than three decades of mineral exploitation, less than 20% of the total canga area was lost. Currently, 21% of the canga area in the CMP is protected by the Campos Ferruginosos National Park. By documenting the initial extent of canga vegetation in the eastern Amazon and the extent to which it has been lost due to mining operations, the results of this work are the first step towards conserving this ecosystem.

Blind Testing: DNA Barcoding Sheds Light Upon the Identity of Plant Fragments as a Subsidy for Cave Conservation.

Plants living above and around caves represent an important, albeit poorly studied, resource within cave ecosystems. The presence of plant material (root-like structures or rhizothemes, saplings, seeds, and seedlings) correlates positively with the biodiversity of the cave dwelling animals as shown for iron-ore caves in Carajás, Pará, Brazil. Plant material collected in caves has proven to be difficult to identify by traditional botanical methods, thus this research aims to provide a qualitative insight into the taxonomy and morphology of rhizothemes and other plant fragments found in the caves. The identification process used a combination of different molecular markers (ITS2, rbcL, and trnH-psbA) followed by a comparison of the sequences obtained against publicly available databases. The rhizothemes were submitted to micromorphological analysis to ascertain their putative root or stem origin and to compare their anatomy with known patterns found in the plant families or genera recovered through molecular matches. All studied samples were Angiosperms, mostly belonging to subclass Rosideae, within four orders: Malpighiales (Euphorbiaceae, Hypericaceae), Sapindales (Anacardiaceae and Sapindaceae), Myrtales (Myrtaceae), Fabales (Fabaceae), and only two belonging to subclass Asteridae, order Gentianales (Apocynaceae). Some of the samples were matched to generic level, with ITS2 being the best marker to identify the fragments because it shows high degree of sequence variation even at specific level and result reliability. All rhizothemes turned out to be roots, and correspondence was found between the existing literature and the individual anatomical patterns for the families and genera retrieved. DNA barcode has proved to be a useful tool to identify plant fragments found in this challenging environment. However, the existence of well curated, authoritatively named collections with ample biological information has proven to be essential to achieve a reliable identification.

Landscape Genomic Conservation Assessment of a Narrow-Endemic and a Widespread Morning Glory From Amazonian Savannas.

Although genetic diversity ultimately determines the ability of organisms to adapt to environmental changes, conservation assessments like the widely used International Union for Conservation of Nature (IUCN) Red List Criteria do not explicitly consider genetic information. Including a genetic dimension into the IUCN Red List Criteria would greatly enhance conservation efforts, because the demographic parameters traditionally considered are poor predictors of the evolutionary resilience of natural populations to global change. Here we perform the first genomic assessment of genetic diversity, gene flow, and patterns of local adaptation in tropical plant species belonging to different IUCN Red List Categories. Employing RAD-sequencing we identified tens of thousands of single-nucleotide polymorphisms in an endangered narrow-endemic and a least concern widespread morning glory (Convolvulaceae) from Amazonian savannas, a highly threatened and under-protected tropical ecosystem. Our results reveal greater genetic diversity and less spatial genetic structure in the endangered species. Whereas terrain roughness affected gene flow in both species, forested and mining areas were found to hinder gene flow in the endangered plant. Finally we implemented environmental association tests and genome scans for selection, and identified a higher proportion of candidate adaptive loci in the widespread species. These mainly contained genes related to pathogen resistance and physiological adaptations to life in nutrient-limited environments. Our study emphasizes that IUCN Red List Criteria do not always prioritize species with low genetic diversity or whose genetic variation is being affected by habitat loss and fragmentation, and calls for the inclusion of genetic information into conservation assessments. More generally, our study exemplifies how landscape genomic tools can be employed to assess the status, threats and adaptive responses of imperiled biodiversity.

Enhancement of anthraquinone production in Morinda citrifolia cell suspension cultures after stimulation of the proline cycle with two proline analogs.

Synthesis of anthraquinones (AQs) involves the shikimate and 2-C-methyl-D-erythritol 4-phosphate pathways. The proline cycle is linked to the pentose phosphate pathway (PPP) to generate NADPH needed in the first steps of this pathway. The effect of two proline analogs, azetidine-2-carboxylic acid (A2C) and thiazolidine-4-carboxylic acid (T4C), were evaluated in Morinda citrifolia suspension cultures. Both analogs gave higher proline accumulation after 6 and 10 days (68 and 179% after 6 days with A2C at 25 and 50 µM, respectively, and 111% with T4C added at 100 µM). Induction of the proline cycle increased the AQ content after 6 days (~40% for 50 µM A2C and 100 µM T4C). Whereas A2C (50 µM) increased only AQ production, T4C also enhanced total phenolics. However, no induction of the PPP was observed with any of the treatments. This pathway therefore does not limit the supply of carbon skeletons to secondary metabolic pathways.

Antinociceptive and anti-inflammatory properties of 7-hydroxycoumarin in experimental animal models: potential therapeutic for the control of inflammatory chronic pain.

OBJECTIVES: In the present study we investigated the antinociceptive, anti-inflammatory and antipyretic effects of 7-hydroxycoumarin (7-HC) in animal models. METHODS: The effects of oral 7-HC were tested against acetic acid-induced writhing, formalin test, tail flick test, complete Freund's adjuvant (CFA)-induced hypernociception, carrageenan-induced paw oedema, lipopolysaccharide-induced fever and the rota rod test. KEY FINDINGS: 7-HC (3-60 mg/kg) produced a dose-related antinociception against acetic acid-induced writhing in mice and in the formalin test. In contrast, treatment with 7-HC did not prevent thermal nociception in the tail flick test. A single treatment with 7-HC, 60 mg/kg, produced a long-lasting antinociceptive effect against CFA-induced hypernociception, a chronic inflammatory pain stimulus. Notably, at 60 mg/kg per day over 4 days the administration of 7-HC produced a continuous antinociceptive effect against CFA-induced hypernociception. 7-HC (30-120 mg/kg) produced anti-inflammatory and antipyretic effects against carrageenan-induced inflammation and lipopolysaccharide-induced fever, respectively. Moreover, 7-HC was found to be safe with respect to ulcer induction. In the rota rod test, 7-HC-treated mice did not show any motor performance alterations. CONCLUSIONS: The prolonged antinociceptive and anti-inflammatory effects of 7-HC, in association with its low ulcerogenic activity, indicate that this molecule might be a good candidate for development of new drugs for the control of chronic inflammatory pain and fever.

Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil.

A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6(T), the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6(T) did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5-4.5 % NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5 %; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA-DNA hybridization data revealed low levels of genomic DNA similarity (less than 30 %) between strain CPDB6(T) and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16 : 1ω7c) and hexadecanoic (16 : 0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6(T) was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6(T) (=CCUG 55948(T)=CCM-A-29:1289(T)) as the type strain.

Phytoremediation potential of the novel atrazine tolerant Lolium multiflorum and studies on the mechanisms involved.

Atrazine impact on human health and the environment have been extensively studied. Phytoremediation emerged as a low cost, environmental friendly biotechnological solution for atrazine pollution in soil and water. In vitro atrazine tolerance assays were performed and Lolium multiflorum was found as a novel tolerant species, able to germinate and grow in the presence of 1 mg kg(-1) of the herbicide. L. multiflorum presented 20% higher atrazine removal capacity than the natural attenuation, with high initial degradation rate in microcosms. The mechanisms involved in atrazine tolerance such as mutation in psbA gene, enzymatic detoxification via P(450) or chemical hydrolysis through benzoxazinones were evaluated. It was demonstrated that atrazine tolerance is conferred by enhanced enzymatic detoxification via P(450). Due to its atrazine degradation capacity in soil and its agronomical properties, L. multiflorum is a candidate for designing phytoremediation strategies for atrazine contaminated agricultural soils, especially those involving run-off avoiding.

Acetylcholinesterase activity of alkaloids from the leaves of Waltheria brachypetala.

Chemical investigation of the leaves of Waltheria brachypetala Turks (Sterculiaceae) resulted in the isolation of quinolinone alkaloids, waltherione-A, waltherione-B (N-methylwaltherione-A), 8-methoxyflindersine, and the cyclic peptide alkaloid waltherine. The inhibition of activity of acetylcholinesterase (AChE) by the alkaloids was evaluated. Waltherione-A, waltherione-B and waltherine showed significant activity.

Expression of Brugmansia candida Hyoscyamine 6beta-Hydroxylase gene in Saccharomyces cerevisiae and its potential use as biocatalyst.

BACKGROUND: Tropane alkaloids, mainly hyoscyamine and scopolamine, are widely used in medicine due to their anticholinergic activity. Scopolamine has a higher demand being the more valuable alkaloid due to its fewer side effects and higher physiological activity. Anisodamine (6beta-hydroxyhyoscyamine) is the intermediate in the conversion of hyoscyamine into scopolamine. Current studies report that this alkaloid is potentially applicable in medicine. The gene that codifies for Hyoscyamine 6-beta hydroxylase, the enzyme responsible for hyoscyamine hydroxylation and epoxidation, leading to scopolamine was isolated from Brugmansia candida. RESULTS: The h6hcDNA was cloned into pYES2.1 and pYES2.1/V5-His-TOPO vectors to produce an untagged and a tagged protein, respectively. The H6H enzyme was produced in Saccharomyces cerevisiae in order to obtain a biological catalyst for potential industrial applications. Protein extracts of the induced yeast were analyzed by Western blot. The expression was detected 4 h after induction and no degradation was observed during the period assayed. The tagged and the untagged proteins were able to transform hyoscyamine, showing a functional expression of the h6hcDNA. CONCLUSION: The strains obtained in this work are promising and potentially applicable in biocatalytic processes.

Immunomodulatory activity of extracts from Cordia superba Cham. and Cordia rufescens A. DC. (Boraginaceae), plant species native from Brazilian Semi-arid / Atividade imunomoduladora de extratos de Cordia superba Cham. and Cordia rufescens A. DC. (Boraginaceae), espécies de plantas nativas do semi-árido brasileiro

The family Boraginaceae is widely distributed in Brazil and in the Northeastern region some species are popularly used to treat symptoms of rheumatism, painful menstruation and dyspepsia. In this work we studied Cordia superba Cham. and C. rufescens A. DC., native from Brazilian Semi-arid region, in order to investigate their immunomodulatory activity. Six extracts were prepared from aerial parts of C. superba and C. rufescens. The cytotoxicity was evaluated using splenocytes from BALB/c mice. The immunomodulatory activity was determined by in vitro assays using activated mouse macrophages and lymphocytes. Peritoneal macrophages obtained from BALB/c mice were stimulated with IFN-gamma and LPS in the presence/absence of the samples. The NO production was measured indirectly through Griess method. Three samples inhibited the production of nitric oxide in values near 50 percent at a concentration of 100 µg/mL. To evaluate the effects of the extracts on lymphocytes, splenocytes from BALB/c mice were incubated with the samples and concanavalin A. Proliferation inhibition was determined by analysis of ³H-thymidine uptake. Samples from the two species had a strong inhibitory activity on lymphocyte proliferation and IL-2 production. Two chloroform extracts prepared from aerial parts of C. rufescens had the lowest IC50 values (7.6 and 11.0 µg/mL).

A família Boraginaceae é amplamente distribuída no Brasil e na região nordeste algumas espécies são usadas popularmente no tratamento de reumatismo, dores menstruais e dispepsias. Neste trabalho foram estudadas as espécies Cordia superba Cham. and C. rufescens A. DC., nativas da região semi-árida brasileira, objetivando investigar a atividade imunomoduladora. Seis extratos foram preparados a partir de partes aéreas das espécies. A citotoxicidade foi avaliada usando culturas de esplenócitos de camundongos BALB/c. A atividade imunomoduladora foi determinada por ensaios in vitro usando macrófagos e linfócitos murinos ativados. Macrófagos peritoneais obtidos de camundongos BALB/c foram estimulados com IFN-gama and LPS na presença/ausência das amostras. A produção de NO foi medida indiretamente através do método de Griess. Três amostras inibiram a produção de NO em valores próximos a 50 por cento (100 µg/mL). Os efeitos das amostras sobre os linfócitos foram avaliados cultivando esplenócitos de camundongos BALB/c em presença destas amostras e de concanavalina A. A proliferação foi determinada pela análise da incorporação de ³H-tritiada. Amostras de duas espécies apresentaram uma forte atividade inibidora sobre a proliferação de linfócitos e sobre a produção de IL-2. Dois extratos clorofórmicos (partes aéreas de C. rufescens) tiveram os menores valores de IC50 (7,6 and 11,0 µg/mL).

Degradation of 2,4-DB in Argentinean agricultural soils with high humic matter content.

The dissipation of 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) in high-humic-matter-containing soils from agricultural fields of the Argentinean Humid Pampa region was studied, employing soil microcosms under different experimental conditions. The added herbicide was dissipated almost completely by soils with and without history of herbicide use by day 28. At 500 ppm, both soils showed the same degradation rates; but at 5-ppm concentration, the chronically exposed soil demonstrated a faster degradation of the herbicide. 2,4-DB addition produced increases in herbicide-degrading bacteria of three and 1.5 orders of magnitude in soils with and without history of herbicide use, respectively, in microcosms with 5 ppm. At 500-ppm concentration, the increase in 2,4-DB degraders was five orders of magnitude after 14 days, independent of the history of herbicide use. No differences were observed in either 2,4-DB degradation rates or in degrader bacteria numbers in the presence and absence of alfalfa plants, in spite of some differential characteristics in patterns of 2,4-DB metabolite accumulation. The main factor affecting 2,4-DB degradation rate would be the history of herbicide use, as a consequence of the adaptation of the indigenous microflora to the presence of herbicides in the field.

Effect of shear stress on anthraquinones production by Rubia tinctorum suspension cultures.

Suspension cultures of Rubia tinctorum, an anthraquinones (AQs) producer, were grown both in Erlenmeyer flasks at 100 rpm and in a 1.5 L mechanically stirred tank bioreactor operating at 450 rpm. The effect of hydrodynamic stress on cell viability, biomass, and AQs production was evaluated. Cell viability showed a transient decrease in the bioreactor during the first days, returning to the initial values toward the end of the culture time. The biomass obtained in the bioreactor was 29% lower than that attained in the Erlenmeyer flasks. The H2O2 production in the bioreactor (with peaks at 7 and 10 days) was about 15 times higher than that obtained in the flasks. A clear relationship exists between the maximum concentration of H2O2 generated and AQs produced. The AQs content in the bioreactor was 233% higher than that in the Erlenmeyer flasks. The AQs specific productivity in the stirred tank and in the Erlenmeyer flasks was 70.7 and 28.5 micromol/g FW/day, respectively. This production capability was maintained in the regrowth assays. On the other hand, the negative effects of hydrodynamic stress on viability and biomass concentration observed in the bioreactor culture were reverted in the regrowth cultures. It can be concluded that R. tinctorum suspension cultures are able to grow in stirred tanks at 450 rpm responding to the hydrodynamic stress with higher concentrations of AQs, which suggest the possibility of a technological approach taking advantage of this phenomenon.

Radical scavenging, antioxidant and cytotoxic activity of Brazilian Caatinga plants.

Extracts of 32 plants from the Brazilian northeastern semi-arid region called Caatinga were evaluated through DPPH radical scavenging assay, beta-carotene bleaching, and brine shrimp lethality tests (BST). Among the extracts studied Byrsonima cf. gardneriana, Mascagnia coriacea, Cordia globosa, Diodia apiculata and Hypenia salzmannii showed the highest activities in DPPH radical scavenging test. In the beta-carotene bleaching test the highest activities were observed for Passiflora cincinnata, Chamaecrista repens, B. cf. gardneriana, Rollinia leptopetala, Serjania glabrata, Diospyros gaultheriifolia, C. globosa, Mimosa ophtalmocentra, M. coriacea and Lippia cf. microphylla. In contrast, R. leptopetala, Zornia cf. brasiliensis and Leonotis nepetifolia were the most active species in the BST.

Dissipation of 2,4-D in soils of the Humid Pampa region, Argentina: a microcosm study.

Phenoxy herbicides like 2,4-dichlorophenoxyacetic acid (2,4-D) are widely used in agricultural practices. Although its half life in soil is 7-14d, the herbicide itself and its first metabolite 2,4-dichlorophenol (2,4-DCP) could remain in the soil for longer periods, as a consequence of its intensive use. Microcosms assays were conducted to study the influence of indigenous microflora and plants (alfalfa) on the dissipation of 2,4-D from soils of the Humid Pampa region, Argentina, with previous history of phenoxy herbicides application. Results showed that 2,4-D was rapidly degraded, and the permanence of 2,4-DCP in soil depended on the presence of plants and soil microorganisms. Regarding soil microbial community, the presence of 2,4-D degrading bacteria was detected even in basal conditions in this soil, possibly due to the adaptation of the microflora to the herbicide. There was an increment of two orders of magnitude in herbicide degraders after 15d from 2,4-D addition, both in planted and unplanted microcosms. Total heterotrophic bacteria numbers were about 1x10(8) CFUg(-1) dry soil and no significant differences were found between different treatments. Overall, the information provided by this work indicates that the soil under study has an important intrinsic degradation capacity, given by a microbial community adapted to the presence of phenoxy herbicides.

Analysis and sequencing of h6hmRNA, last enzyme in the tropane alkaloids pathway from anthers and hairy root cultures of Brugmansia candida (Solanaceae)

Brugmansia candida (Solanaceae) is a native tree distributed across South-American and produces the pharmacologically- important group of tropane alkaloids including scopolamine. This biocompound is synthesised from hyoscyamine by action of Hyoscyamine 6-â hydroxylase (H6H, EC 1.14.11.11) at the end of the tropane alkaloid pathway. Here are reported the tissue and organ-specific expression of h6hmRNA by RT-PCR analyses and the isolation, cloning and sequencing of the cDNA obtained from B. candida anthers and hairy root transformed cultures. Bioinformatic analysis of the nucleotide sequence revealed an uninterrupted ORF of 1038 bp and the predicted aminoacid sequence could be 344 aminoacid long. A database search showed that this sequence has high homology (97 percent identity) to Hyoscyamus niger H6H protein (Genbank accession number AAA33387.1).

Phytoremediation of 2,4-dichlorophenol by Brassica napus hairy root cultures.

We have obtained hairy root cultures of Brassica napus with high biomass and genetic stability which produce peroxidases, enzymes involved in biodegradation processes. In this work, these hairy root cultures were used to study the removal of 2,4-dichlorophenol (2,4-DCP), a common contaminant in industrial effluents that is highly toxic for human and aquatic life. The optimum conditions to obtain high efficiency in the removal process were established. Roots were able to remove 2,4-DCP from aqueous solutions containing 100-1000 mg/l, in the presence of H(2)O(2) concentrations ranging from 5 to 10 mM. After a short period of incubation (15 min), high removal efficiencies were achieved (91-94%) and maximal removal, of approx. 97-98%, was obtained with 1 h of reaction. High removal efficiencies (93-95%) were observed in a broad pH range (pH 3-9), reaching 98-99% in the range pH 4-8. Moreover, roots could be re-used, almost for six consecutive cycles, to remove 2,4-DCP. The oxidation catalysed by peroxidases would be the main mechanism involved in this process. The results suggest that these cultures could be useful tools for phytoremediation.

In vitro procuction of scopolamine and hyoscyamine: influence of different elicitors on hairy root cultures of Brugmansia candida

The tropane alkaloids scopolamine and hyoscyamine arestill extracted from plants that belong to several species of Solanaceae because their chemical syntesis is difficult and expensive. These anticholinergic agents are employed in medicine as antispasmodics, preoperative medication and for the treatment of motion sickness. In our laboratory, hairy roots of Brugmansia candida, a South American plant which both alkaloids, were obtained through transformation with Agrobacterium rhizogenes and cultured in vitro. To increase the productivity of the cultures, these were exposed to different elicitors: CaCl2, salicylic acid and autoclaved roots of B. candida. The effects on growth, alkaloid accumulation and release into the medium were evaluated. CaCl2 at 50.00 and 100.00 mM, increased the accumulation of scopolamine and hyoscyamine after 24 hours ( 30-60per cent), while after 48 hour levels of 50.00 mM decreased their accumulation ( 50per cent). No effect was observed on release of alkaloids into the medium. Salicylic acid, a compound involved in plant defense, at 0.01 and 1.00 mM increased accumulation of booth alkaloids (ranging from 30 to 170 per cent), particularly after 24 and 48 hours. There was also increase in the release of scopolamine and hyoscyamine into the medium. The homogenized roots had a positive effect on alkaloid accumulation in the roots throughout the experiment (ranging from 100 to 500 per cent). This was most noticeable for hyoscyamine, particulary after 24 and 72 hours of exposition. The results seen with homogenized roots are probably due to endogenous elicitors which are liberated in the subsequent steps of autoclaving and sonication.