Microbial hitchhikers on intercontinental dust: high-throughput sequencing to catalogue microbes in small sand samples

Microbiological studies on the intercontinental transport of dust are confounded by the difficulty of obtaining sufficient material for analysis. Axenic samples of dust collected at high altitudes or historic specimens in museums are often so small and precious that the material can only be sacrificed when positive results are assured. With this in mind, we evaluated current methods and developed new ones in an attempt to catalogue all microbes present in small dust or sand samples. The methods used included classical microbiological approaches in which sand extracts were plated out on a variety of different media, polymerase chain reaction (PCR)-based amplification of 16S/18S rRNA sequences followed by construction of clone libraries, PCR amplification of 16S rRNA sequences followed by high-throughput sequencing (HtS) of the products and direct HtS of DNA extracted from the sand. A representative sand sample collected at Bahaï Wadi in the desert of the Republic of Chad was used. HtS with or without amplification showed the most promise and can be performed on ≤100ng DNA. Since living microbes are often required, current best practices would involve geochemical and microscopic characterisation of the sample, followed by DNA isolation and direct HtS. Once the microbial content of the sample has been deciphered, growth conditions (including media) can be tailored to isolate the micro-organisms of interes

Surface enhanced Raman scattering (SERS)-active bacterial detection by layer-by-layer (LbL) assembly all-nanoparticle microcapsules

Polymeric microcapsules composed by the Layer-by-Layer (LbL) approach have been used for various applications including drug delivery into cells and in vivo, conducting enzyme catalyzed reactions, performing sensoric functions. Typically, LbL-assembled microcapsules have been formulated via alternating deposition of positively and negatively charged polyelectrolytes onto sacrificial templates or so-called cores. In this work, we extend the LbL assembly to produce microcapsules solely based on nanoparticles instead of polymers. We have identified that 5 layers of nanoparticles is the minimum number of layers for a stable assembly of capsules on calcium carbonate templates. Subsequently, these capsules comprised of nanoparticles were applied as Surface Enhanced Raman Scattering (SERS) platform, where the nanoparticle-based shell of capsules is shown to enable SERS of both solutes and macromolecular structures such as bacterial cells

Hollow silver alginate microspheres for drug delivery and surface enhanced Raman scattering detection

Multifunctional silver alginate hydrogel microspheres are assembled via a template assisted approach using calcium carbonate cores. Sodium alginate is immobilized into the highly porous structure of calcium carbonate microspheres followed by cross-linking in the presence of silver ions. The simultaneous processes of the growth of silver nanoparticles in the alginate matrix and the removal of the calcium carbonate template are triggered by ascorbic acid. The abundance of silver nanoparticles and their interparticular junctions in the alginate network allow for the detection of solutes using Raman spectroscopy using the surface of the plasmonic microspheres. Rhodamine B was used to illustrate the potential applications of such multifunctional plasmonic alginate hydrogel microspheres for sensing at low concentrations. A proof of principle for using such particles for the quick identification of microorganisms is then demonstrated using the Escherichia coli bacterium

Weathering-Associated Bacteria from the Damma Glacier Forefield: Physiological Capabilities and Impact on Granite Dissolution ▿

Several bacterial strains isolated from granitic rock material in front of the Damma glacier (Central Swiss Alps) were shown (i) to grow in the presence of granite powder and a glucose-NH4Cl minimal medium without additional macro- or micronutrients and (ii) to produce weathering-associated agents. In particular, four bacterial isolates (one isolate each of Arthrobacter sp., Janthinobacterium sp., Leifsonia sp., and Polaromonas sp.) were weathering associated. In comparison to what was observed in abiotic experiments, the presence of these strains caused a significant increase of granite dissolution (as measured by the release of Fe, Ca, K, Mg, and Mn). These most promising weathering-associated bacterial species exhibited four main features rendering them more efficient in mineral dissolution than the other investigated isolates: (i) a major part of their bacterial cells was attached to the granite surfaces and not suspended in solution, (ii) they secreted the largest amounts of oxalic acid, (iii) they lowered the pH of the solution, and (iv) they formed significant amounts of HCN. As far as we know, this is the first report showing that the combined action of oxalic acid and HCN appears to be associated with enhanced elemental release from granite, in particular of Fe. This suggests that extensive microbial colonization of the granite surfaces could play a crucial role in the initial soil formation in previously glaciated mountain areas

Data publication: Uranium (VI) reduction by an iron-reducing Desulfitobacterium species as single cells and in artificial multispecies bio-aggregates

The stored data sets represent both the raw data and the evaluated data that were used for the publication about speciation-dependent uranium(VI) reduction by an iron-reducing bacteria in both pure culture and artificial multispecies bio-aggregates

Biocarriers Improve Bioaugmentation Efficiency of a Rapid Sand Filter for the Treatment of 2,6-Dichlorobenzamide-Contaminated Drinking Water

Aminobacter sp. MSH1 immobilized in an alginate matrix in porous stones was tested in a pilot system as an alternative inoculation strategy to the use of free suspended cells for biological removal of micropollutant concentrations of 2,6-dichlorobenzamide (BAM) in drinking water treatment plants (DWTPs). BAM removal rates and MSH1 cell numbers were recorded during operation and assessed with specific BAM degradation rates obtained in lab conditions using either freshly grown cells or starved cells to explain reactor performance. Both reactors inoculated with either suspended or immobilized cells showed immediate BAM removal under the threshold of 0.1 μg/L, but the duration of sufficient BAM removal was 2-fold (44 days) longer for immobilized cells. The longer sufficient BAM removal in case of immobilized cells compared to suspended cells was mainly explained by a lower initial loss of MSH1 cells at operational start due to volume replacement and shear. Overall loss of activity in the reactors though was due to starvation, and final removal rates did not differ between reactors inoculated with immobilized and suspended cells. Management of assimilable organic carbon, in addition to cell immobilization, appears crucial for guaranteeing long-term BAM degradation activity of MSH1 in DWTP units.status: publishe

Biocarriers Improve Bioaugmentation Efficiency of a Rapid Sand Filter for the Treatment of 2,6-Dichlorobenzamide-Contaminated Drinking Water

Aminobacter sp. MSH1 immobilized in an alginate matrix in porous stones was tested in a pilot system as an alternative inoculation strategy to the use of free suspended cells for biological removal of micropollutant concentrations of 2,6-dichlorobenzamide (BAM) in drinking water treatment plants (DWTPs). BAM removal rates and MSH1 cell numbers were recorded during operation and assessed with specific BAM degradation rates obtained in lab conditions using either freshly grown cells or starved cells to explain reactor performance. Both reactors inoculated with either suspended or immobilized cells showed immediate BAM removal under the threshold of 0.1 μg/L, but the duration of sufficient BAM removal was 2-fold (44 days) longer for immobilized cells. The longer sufficient BAM removal in case of immobilized cells compared to suspended cells was mainly explained by a lower initial loss of MSH1 cells at operational start due to volume replacement and shear. Overall loss of activity in the reactors though was due to starvation, and final removal rates did not differ between reactors inoculated with immobilized and suspended cells. Management of assimilable organic carbon, in addition to cell immobilization, appears crucial for guaranteeing long-term BAM degradation activity of MSH1 in DWTP units