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  • Springer  (5)
  • American Chemical Society  (2)
  • 2020-2023  (7)
  • 1980-1984
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  • 2021  (7)
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  • 1
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    Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics (2021)
    American Chemical Society
    In:  ACS Chemical Biology .
    Details
    Publication Date: 2022-01-07
    Description: While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. This demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.
    Type: Article , PeerReviewed
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  • 2
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    Geochemical and isotopic insights into the assembly, evolution and disruption of a magmatic plumbing system before and after a cataclysmic caldera-collapse eruption at Ischia volcano (Italy) (2021)
    Springer
    Details
    Publication Date: 2022-04-22
    Description: New geochemical and isotopic data on volcanic rocks spanning the period ~75–50 ka BP on Ischia volcano, Italy, shed light on the evolution of the magmatic system before and after the catastrophic, caldera-forming Monte Epomeo Green Tuff (MEGT) eruption. Volcanic ac tivity during this period was influenced by a large, composite and differentiating magmatic system, replenished several times with isotopically distinct magmas of deepprovenance. Chemical and isotopic variations highlight that the pre-MEGT eruptions were fed by trachytic/phonolitic magmas from an isotopically zoned reservoir that were poorly enriched in radiogenic Sr and became progressively less radiogenic with time. Just prior to the MEGT eruption, the magmatic system was recharged by an isotopically distinct magma, relatively more enriched in radiogenic Sr with respect to the previously erupted magmas. This second magma initially fed several SubPlinian explosive eruptions and later supplied the climactic, phonolitic-to-trachytic MEGT eruption(s). Isotopic data, together with erupted volume estimations obtained for MEGT eruption(s), indicate that 〉5–10 km3of this relatively enriched magma had accumulated in the Ischia plumbing system. Geochemical modelling indicates that it accumulated at shallow depths (4–6 km), over a period of ca. 20 ka. After the MEGT eruption, volcanic activity was fed by a new batch of less differentiated (trachyte-latite) magma that was slightly less enriched in radiogenic Sr. The geochemical and Sr–Nd-isotopic variations through time reflect the upward flux of isotopically distinct magma batches, variably contaminated byHercynian crust at 8–12 km depth. The deep-sourced latitic to trachytic magmas stalled at shallow depths (4–6 km depth), differentiated to phonolite through crystal fractionation and assimilation of a feldspar-rich mush, or ascended directly to the surface and erupted.
    Description: Published
    Description: 1035
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: Ischia volcano ; Magmatic plumbing system ; Radiogenic isotopes ; Geothermometry ; Feldspar assimilation ; Caldera collapse
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Groundwater of Sicily (Italy) Close to Landfill Sites: Quality and Human Health Risk Assessment (2021)
    Springer
    Details
    Publication Date: 2021-12-10
    Description: Groundwater close to three municipal solid waste landfll sites in Sicily (southern Italy) was sampled to determine the presence of contaminants and the risk associated with its possible use as drinking and sanitary water. Polycyclic aromatic hydrocarbons, polychlorinated biphenyls, polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, and metals were investigated. These target compounds are the most common pollutants present in leachates. Risk Assessment Guidance for Superfund (RAGS, US EPA) was used to assess human health risk. Ingestion, dermal, and total exposure to these xenobiotic contaminants in groundwater were evaluated, and the cancer and non-cancer risk indexes were calculated. The results revealed that, while the groundwater complied with Italian Drinking Water Directive 30/2001, it did not comply with the "good environmental state" criteria of Directive 30/2009 at two of the three sites investigated. Worrying results were revealed by the risk assessment at the investigated sites. Cancer and non-cancer risk indexes indicated a probable risk, mainly due to dermal exposure to groundwater. These results underline the importance of assessing the risk for all possible routes, evaluating not only ingestion but also dermal exposure, especially when organic pollutants are present. The results of this study show that human health risk has probably been underestimated in the past, as dermal exposure to organic pollutants has only rarely been evaluated in the literature.
    Description: Published
    Description: 535–550
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: Human health risk ; Polycyclic aromatic hydrocarbons ; Polychlorinated biphenyls ; Dioxin PCDD/Fs ; Toxic elements ; Environmental quality standard
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Geochemical characterisation of the thermo-mineral waters of Greece (2021)
    Springer
    Details
    Publication Date: 2022-06-22
    Description: Geothermal areas of Greece are located in regions affected by recent volcanism and in continental basins characterised by elevated heat flow. Many of them are found along the coast and thus, water is often saline due to marine intrusion. In the current study, we present about 300 unpublished and literature data from thermal and cold mineral waters collected along Greece. Samples were analysed for major ions, Li, SiO2 and isotopes in water. Measured temperatures range from 6.5 to 98°C, pH from 1.96 to 11.98, whilst Total Dissolved Solutes (TDS) from 0.22 to 51 g/L. Waters were subdivided into four main groups: i) thermal; ii) cold; iii) acidic (pH 〈5) and iv) hyperalkaline (pH 〉11). On statistical basis, the thermal waters were subdivided into subgroups according to both their temperature [warm (〈29 °C), hypothermal (29-48 °C), thermal (48-75 °C) and hyperthermal (〉75 °C)] and TDS [low salinity (〈4 g/L), brackish (4-30 g/L) and saline (〉30 g/L)]. Cold waters were subdivided basing on their pCO2 [low (〈0.05 atm), medium (0.05-0.85 atm) and high (〉0.85 atm)]. δ18O-H2O ranges from -12.7 to +2.7 ‰ vs. SMOW, while δ2H-H2O from -91 to +12 ‰ vs. SMOW being generally comprised between the Global Meteoric Water Line and the East Mediterranean Meteoric Water Line. Positive δ18O shifts with respect to the former are mostly related to mixing with seawater, while only for a few samples they point to high-temperature water-rock interaction processes. Only a few thermal waters gave reliable geothermometric estimates, suggesting reservoir temperatures between 80 and 260 °C.
    Description: Published
    Description: 2111–2133
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: Hydrogeochemistry ; Stable isotopes ; Carbon dioxide ; Geothermometry ; 03. Hydrosphere ; 03.04. Chemical and biological
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Toward a global reference database of COI barcodes for marine zooplankton (2021)
    Springer
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bucklin, A., Peijnenburg, K. T. C. A., Kosobokova, K. N., O'Brien, T. D., Blanco-Bercial, L., Cornils, A., Falkenhaug, T., Hopcroft, R. R., Hosia, A., Laakmann, S., Li, C., Martell, L., Questel, J. M., Wall-Palmer, D., Wang, M., Wiebe, P. H., & Weydmann-Zwolicka, A. Toward a global reference database of COI barcodes for marine zooplankton. Marine Biology, 168(6), (2021): 78, https://doi.org/10.1007/s00227-021-03887-y.
    Description: Characterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.
    Description: Funding sources for authors of the review paper are described here: Scientific Committee on Oceanic Research (SCOR), and a grant to SCOR from the U.S. National Science Foundation (OCE-1840868). Netherlands Organization for Scientific Research (NWO) Vidi Grant/Award Number: 016.161.351 to K.T.C.A.P. European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 746186 (POSEIDoN) to D.W.P. The work of K.N.K. was performed in the framework of the state assignment of IO RAS (Theme No. 0128-2021-0007) and partially supported by Russian Foundation for Basic Research grants No. 18-05-60158 and No. 19-04-00955. The work of A.W.Z. was supported by a grant from HIDEA—Hidden diversity of the Arctic Ocean (No. 2017/27/B/NZ8/01056) from the National Science Centre, Poland, and a Fulbright Senior Award. The Norwegian Taxonomy Initiative of the Norwegian Biodiversity Information Centre provided funding for A.H. and L.M. (Project Nos. 70184233/HYPNO and 70184240/NORHYDRO), and for T.F. (Project Nos. 70184233/COPCLAD and 70184241/HYPCOP). The work of R.R.H. and J.M.Q. was supported by Census of Marine Life and NOAA Ocean Exploration and Research (NA05OAR4601079 and NA15OAR0110209). The work of S.L. was conducted at the Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB). HIFMB is a collaboration between the Alfred-Wegener-Institute, Helmholtz-Center for Polar and Marine Research, and the Carl-von-Ossietzky University Oldenburg, initially funded by the Ministry for Science and Culture of Lower Saxony and the Volkswagen Foundation through the Niedersächsisches Vorab’ grant program (Grant No. ZN3285).
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Watershed suspended sediment supply and potential impacts of dam removals for an estuary (2021)
    Springer
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ralston, D. K., Yellen, B., & Woodruff, J. D. Watershed suspended sediment supply and potential impacts of dam removals for an estuary. Estuaries and Coasts, (2021), https://doi.org/10.1007/s12237-020-00873-3.
    Description: Observations and modeling are used to assess potential impacts of sediment releases due to dam removals on the Hudson River estuary. Watershed sediment loads are calculated based on sediment-discharge rating curves for gauges covering 80% of the watershed area. The annual average sediment load to the estuary is 1.2 Mt, of which about 0.6 Mt comes from side tributaries. Sediment yield varies inversely with watershed area, with regional trends that are consistent with substrate erodibility. Geophysical and sedimentological surveys in seven subwatersheds of the Lower Hudson were conducted to estimate the mass and composition of sediment trapped behind dams. Impoundments were classified as (1) active sediment traps, (2) run-of-river sites not actively trapping sediment, and (3) dammed natural lakes and spring-fed ponds. Based on this categorization and impoundment attributes from a dam inventory database, the total mass of impounded sediment in the Lower Hudson watershed is estimated as 4.9 ± 1.9 Mt. This represents about 4 years of annual watershed supply, which is small compared with some individual dam removals and is not practically available given current dam removal rates. More than half of dams impound drainage areas less than 1 km2, and play little role in downstream sediment supply. In modeling of a simulated dam removal, suspended sediment in the estuary increases modestly near the source during discharge events, but otherwise effects on suspended sediment are minimal. Fine-grained sediment deposits broadly along the estuary and coarser sediment deposits near the source, with transport distance inversely related to settling velocity.
    Description: This work was sponsored by the National Estuarine Research Reserve System Science Collaborative, which is funded by the National Oceanic and Atmospheric Administration and managed by the University of Michigan Water Center (NAI4NOS4190145). Additional support for participating graduate and undergraduates was provided by the Northeast Climate and Adaptation Center and the Hudson River Fund. Additional support for DKR was provided by the Hudson River Foundation (Grant No. 003/19A). Data from sediment cores that were collected in association with this manuscript are archived here: https://doi.org/10.7275/dh3v-0x33.
    Keywords: Dam removal ; Suspended sediment ; Watershed sediment yield ; Sediment supply ; Sediment trapping
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Differences in Leaf Chemistry and Glandular Trichome Density between Wild Southwestern American Hop ( Humulus neomexicanus ) and Commercial Hop Cultivars (2021)
    American Chemical Society
    In:  Journal of Agricultural and Food Chemistry, 69 (27). pp. 7798-7814.
    Details
    Publication Date: 2022-01-07
    Description: The female flowers (“cones”) of the hop plant (Humulus L.) produce compounds that contribute to the flavor and other properties of beer. Hop leaves and cones produce many of the same compounds, which also confer agronomic traits such as insect and disease resistance. Targeted and untargeted ultraperformance liquid chromatography-quadrupole time-of-flight–mass spectrometry with Waters MSE technology (UPLC-QTof-MSE) metabolomics were used to compare leaf phytochemical compositions of greenhouse-grown southwestern American wild Humulus neomexicanus (A. Nelson and Cockerell) Rydb. against a group of commercial hop cultivars consisting of both pure European Humulus lupulus L. and European–North American hybrids. Principal component analysis showed a clear distinction in chemical profiles between the two groups. H. neomexicanus leaves had a significantly higher content of total α acids (p = 4.4 × 10–9), total bitter acids (p = 2.6 × 10–6), cohumulone (p = 1.0 × 10–13), humulone + adhumulone (p = 9.1 × 10–4), and the prenylflavonoids xanthohumol (p = 0.013) and desmethylxanthohumol (p = 0.029) as well as significantly higher densities of glandular trichomes (p = 1.3 × 10–6), the biosynthetic site of those compounds. Most flavonol glycosides measured were also significantly more abundant in H. neomexicanus (p = 1.5 × 10–22 to 0.0027), whereas phenolic acids were consistently, but generally nonsignificantly (p 〉 0.05), more abundant in the cultivars. The higher bitter acid, prenylflavonoid, and flavonol glycoside content of H. neomexicanus leaves may help to confer more favorable insect and disease-resistance properties.
    Type: Article , PeerReviewed
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