Soil organic carbon cycling in a long-term agricultural experiment,Switzerland

Soils are one of the largest organic carbon pools and changes in the carbon release from soils has considerable impact on the composition of atmospheric CO2. Alongside the accelerated carbon release from soils by anthro-pogenic warming (Crowther et al., 2016), agricultural use strongly affects soil organic carbon (SOC) (Johnstonet al., 2009). Conversion from conventional to organic farming has been suggested a valuable contribution to sequester SOC providing a great mitigation potential within agricultural practices (Smith et al., 2008).Here we present SOC contents and 14C activity under two different farming practices in the long-termagricultural DOK trial at Therwil, Switzerland (Mäder et al., 2002). In this long-lasting agricultural experiment, we compare biodynamic farming (biodyn), which receives manure and biodynamic preparations, with conventional farming (conmin), which receives only mineral fertilizers. We analyzed functional SOC fractions from both farming practices for SOC concentration and radiocarbon (∆14C) in two soil layers (0-20 cm and 20-50 cm).Three SOC fractions were obtained by density and particle size fractionation: particular organic matter (POM,labile pool), mineral-associated organic matter 20μm (MOM >20μm, labile pool).Our results clearly show higher SOC concentrations for biodyn compared to conmin in all SOC fractions in the upper soil layer (0-20 cm). In the subsoil (20-50 cm) we found a negligible influence of farming practices with depth. High ∆14C values in the POM and >20μm fraction indicated that they are a more labile and fastcycling carbon pool, whereas lower∆14C values in the 20μm fraction, with higher ∆14C values in the biodyn system suggesting greater input of fresh plant material with a faster turnover

Using pre-screening methods for an effective and reliable site characterization at megasites

This paper illustrates the usefulness of pre-screening methods for an effective characterization of polluted sites. We applied a sequence of site characterization methods to a former Soviet military airbase with likely fuel and benzene, toluene, ethylbenzene, and xylene (BTEX) contamination in shallow groundwater and subsoil. The methods were (i) phytoscreening with tree cores; (ii) soil gas measurements for CH(4), O(2), and photoionization detector (PID); (iii) direct-push with membrane interface probe (MIP) and laser-induced fluorescence (LIF) sensors; (iv) direct-push sampling; and (v) sampling from soil and from groundwater monitoring wells. Phytoscreening and soil gas measurements are rapid and inexpensive pre-screening methods. Both indicated subsurface pollution and hot spots successfully. The direct-push sensors yielded 3D information about the extension and the volume of the subsurface plume. This study also expanded the applicability of tree coring to BTEX compounds and tested the use of high-resolution direct-push sensors for light hydrocarbons. Comparison of screening results to results from conventional soil and groundwater sampling yielded in most cases high rank correlation and confirmed the findings. The large-scale application of non- or low-invasive pre-screening can be of help in directing and focusing the subsequent, more expensive investigation methods. The rapid pre-screening methods also yielded useful information about potential remediation methods. Overall, we see several benefits of a stepwise screening and site characterization scheme, which we propose in conclusion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11356-015-4649-6) contains supplementary material, which is available to authorized users

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR

Petrology and mineral chemistry of sulphide ores and associated metalliferous rocks of the Gamsberg Zn-Pb deposit, South Africa : implications for ore genesis and mineral exploration

Thesis (PhD)--University of Stellenbosch, 2004.ENGLISH ABSTRACT: The Gamsberg Zn-Pb deposit is a metamorphosed and multiply deformed sediment-hosted base metal deposit in the central Namaqua Province of South Africa. The deposit is hosted by the Bushmanland Group, a late Palaeoproterozoic (2000-1600 Ma) supracrustal succession of quartzite, metapelitic schist and interbedded metavolcanic rocks. Mineralisation occurs within the central part of the Gams Formation, a heterogeneous sequence of metamorphosed metalliferous sediments and fine-grained organic-rich shales. The ore horizon is subdivided into a lower unit of metapelite-hosted ore, an intermediate layer of phosphorite-hosted ore, and an upper unit of banded garnet-apatite ore. The ore body is enveloped by unmineralised silicate-, carbonate- and oxide-facies metalliferous rocks, which originally represented mixtures of Fe-Mn-rich hydrothermal precipitates, authigenic carbonate, and variable concentrations of detrital material. Based on mineralogical and geochemical characteristics, the metalliferous host rocks are subdivided into iron formations, coticules, Fe-Mn silicates, impure marbles and barite/Ba-rich quartzite. Minerals of the Gams Formation mostly represent solid solution between the Fe and Mn end-members of garnet, pyroxene, pyroxenoid, amphibole, olivine, spinel and ilmenite. Calcium-rich rock types are a typical feature and characterized by the occurrence of manganoan calcite, clinopyroxene, andradite-rich garnet and titanite. A successive increase in the (Mn+Ca):Fe value of rocks and minerals is evident with increasing distance from the ore horizon. Amphibole is restricted to Fe-rich ore-bearing assemblages, whereas orthopyroxene, clinopyroxene, Fe-rich pyroxenoid and olivine are present in intermediate assemblages, and Mn-rich rhodonite and pyroxmangite in the most manganiferous assemblages. These variations are mimicked by an increase in the Mn:Fe value of coexisting garnet and ilmenite group minerals with increasing distance from ore. LA-ICP-MS analyses have been used to constrain the REE patterns of garnet and apatite. In the ore-body, these minerals display a positive Eu anomaly, which is interpreted to reflect a distinct hydrothermal signature. In contrast, garnet and apatite in unmineralised metalliferous rocks display nil or a negative Eu anomaly. Primary features of the Gams Formation, such as REE patterns, the banded nature of garnet-apatite ore, the presence of diagenetic apatite nodules, and the distribution of the redox-sensitive elements Ba and Mn have been used to constrain palaeo-environmental conditions. The results indicate that metapelitehosted ore has been deposited in a stratified ocean that was characterised by anoxic bottom waters and precipitation of Fe and Zn sulphides into organic matter-rich shales. These rocks were superceded by phosphorite-hosted ore, garnet-apatite ore and metalliferous host rocks that developed in a suboxic to oxic environment. The large size of the deposit, the internal lamination of the ores and the predominance of sphalerite and barite are consistent with a vent-distal setting and precipitation of the ore-forming constituents from dense and reduced hydrothermal fluids, which originated due to reactivation of dormant growth faults. Collectively, the geological evidence indicates that Gamsberg is bridging the gap betweenthe SEDEX and BHT classifications. The relationships demonstrate that differences between these two classes of sediment-hosted Zn-Pb deposits are predominantly related to environmental conditions within localised third order basins and not to fundamental differences in ore-forming processes.AFRIKAANSE OPSOMMING: Die Gamsberg Zn-Pb afsetting is ‘n meerfasig vervormde en gemetamorfiseerde sedimentgesetelde onedel metaal afsetting in die sentrale Namakwa Provinsie van Suid Afrika. Die afsetting word geherberg deur die Boesmanland Groep, ‘n laat Paleoproterosoïse (2000 – 1600 Ma) bokors-opeenvolging van kwartsiet, metapelitiese skis en tussengelaagde metavulkaniese gesteente. Mineralisasie word gevind in the sentrale deel van die Gams Formasie. Die Gams Formasie is ‘n heterogene opeenvolging van gemetamorfiseerde metaalhoudende sediment en fynkorrelrige organiese skalie. Die erts horison word onderverdeel in ‘n onderste laag van metapeliet-gesetelde erts, n sentrale laag van fosforiet-gesetelde erts, en ‘n boonste laag van gebande granaat-apatiet erts. Die erts-liggaam word omhuls deur ongemineraliseerde silikaat-, karbonaat- en oksied-fasies metal-ryke rotse. Hierdie gesteentes word geinterpreteer as oorspronklike mengsels van Fe-Mn-ryke hidrotermale partikels, outigeniese karbonaat, en verskeie hoeveelhede detritale materiaal. Gebaseer op mineralogiese en geochemiese kenmerke word hierdie rotse onderverdeel in ysterformasies, „coticules“, Fe-Mn silikate, onsuiwer marmer en barite/Ba-ryke kwartsiet. Minerale van die Gams Formasie form meestal soliede oplossingsreekse tussen die Fe en Mn endlede van granaat, pirokseen, piroksenoid, amfibool, olivien, spinel en ilmeniet. Kalsium-ryke rots tipes is ‘n tipiese kenmerk van die Gams Formasie en word gekenmerk deur mangaan-ryke kalsiet, klinopirokseen, andradiet-ryke granaat en sfeen. Daar word ‘n stapsgewyse vergroting van die (Mn+Ca):Fe verhouding in gesteentes en minerale gevind met toeneemende afstand van die erts horison. Amfibool is beperk tot Fe-ryke ertsdraende gesteentes, ortopirokseen, klinopirokseen, Fe-ryke piroksenoid en olivien tot intermediêre gesteentes, en Mn-ryke rodoniet en piroksmangiet tot Mn-ryke gesteentes. Hierdie variasies gaan gepaard met vergroting van die Mn:Fe verhouding in granaat en ilmeniet-groep minerale met toeneemende afstand van die erts. LA-ICP-MS analises was gebruik om die skaars-aarde element patrone van granaat en apatiet te bepaal. In die erts-liggaam wys hierdie minerale ‘n positiewe Eu anomalie, wat geinterpreteerd word as ‘n hidrotermale kenmerk. In ongemineraliseerde gasheer gesteentes wys granaat en apatiet geen of ‘n negatiewe Eu anomalie. Primêre kenmerke van die Gams Formasie, soos skaars-aarde patrone, the gebande voorkoms van granaat-apatiet erts, die teenwoordigheid van diagenetiese apatiet knolle, en die verspreiding van die redox-sensitiewe elemente Ba en Mn, was gebruik om afleidings oor die paleo-omgewing te maak. Die resultate het gewys dat metapeliet-gesetelde erts afgeset was onder anoksiese bodem water deur presipitasie van Fe en Zn sulfiedes in organiese skalie. Hierdie erts gaan oor in fosforiet-gesetelde erts, granaat-apatiet erts en metaal-ryke gasheer gesteente wat in ‘n suboksiese tot oksiese omgewing ontstaan het. Die grootte van die afsetting, die interne gelaagdheid van die erts, asook die teenwoordigheid van sfaleriet en bariet dui op ‘n distale omgewing relatief tot die hidrotermale bron en presipitasie van die ertsuit digte en gereduseerde hidrotermale vloeistowwe, wat ontstaan het deur die heraktiveering van rustende groeiverskuiwings. Gesaamentlik bewys die geologiese kenmerke van Gamsberg dat gemetamorfiseerde SEDEX en Broken Hill-tipe mineralisasie binne die perke van ‘n enkele afsetting kan voorkom. Die geologiese verhoudings dui aan dat verskille tussen hierdie twee tipes van sedimentgesetelde afsettings meestal veroorsaak word deur omgewings-toestande binne in gelokaliseerde derde orde komme en nie deur fundamentele verskille in ertsvormende prosesse nie