Bacterial Communities from the Copper Mine of Wettelrode (Germany).

Bacterial communities from three different sampling sites of a copper mine tunnel were characterized by 16S rRNA sequencing (NGS). A high presence of halophilic bacteria was confirmed by comparison with literature data and with reference samples from other highly salt-exposed soils. Among others, high read numbers of , , , , , and uncultivated strains of , , , and were found.

Soil Bacteria in Archaeology: What Could Rank Abundance Functions Tell Us About Ancient Human Impacts on Microbial Communities?

Metagenomic analysis of soil bacterial communities based on 16S rRNA reflects a typical community composition containing a low number of high-abundance types and a very high number of low-abundance types. Here, the formation of characteristic rank order functions of bacterial abundance is investigated by modelling the dynamics of soil bacterial communities, assuming a succession of different bacterial populations that grow rapidly and decay more slowly. We found that the characteristic shape of typical rank order functions is well reflected by simulations.

A droplet-based microfluidic platform enables high-throughput combinatorial optimization of cyanobacterial cultivation.

Cyanobacteria are fast-growing, genetically accessible, photoautotrophs. Therefore, they have attracted interest as sustainable production platforms. However, the lack of techniques to systematically optimize cultivation parameters in a high-throughput manner is holding back progress towards industrialization.

From Microtiter Plates to Droplets-There and Back Again.

Droplet-based microfluidic screening techniques can benefit from interfacing established microtiter plate-based screening and sample management workflows. Interfacing tools are required both for loading preconfigured microtiter-plate (MTP)-based sample collections into droplets and for dispensing the used droplets samples back into MTPs for subsequent storage or further processing. Here, we present a collection of Digital Microfluidic Pipetting Tips (DMPTs) with integrated facilities for droplet generation and manipulation together with a robotic system for its operation.

Microtoxicology by microfluidic instrumentation: a review.

Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies.

Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data.

The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera.

Microfluidically supported characterization of responses of Rhodococcus erythropolis strains isolated from different soils on Cu-, Ni-, and Co-stress.

We present a new methodological approach for the assessment of the susceptibility of Rhodococcus erythropolis strains from specific sampling sites in response to increasing heavy metal concentration (Cu, Ni, and Co) using the droplet-based microfluid technique. All isolates belong to the species R. erythropolis identified by Sanger sequencing of the 16S rRNA.

Reclassification of as gen. nov., comb. nov., of as comb. nov, with an emended description of the genus , recognition that the genus names and are heterotypic synonyms and description of sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter.

In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300 developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7-8 and with 0.5-2 % (m/v) NaCl.

Droplet-Based Screening for the Investigation of Microbial Nonlinear Dose-Response Characteristics System, Background and Examples.

Droplet-based microfluidics is a versatile tool to reveal the dose-response relationship of different effectors on the microbial proliferation. Traditional readout parameter is the temporal development of the cell density for different effector concentrations. To determine nonlinear or unconventional dose-response relationships, data with high temporal resolution and dense concentration graduation are essential.

Microfluidic Chamber Design for Controlled Droplet Expansion and Coalescence.

The defined formation and expansion of droplets are essential operations for droplet-based screening assays. The volumetric expansion of droplets causes a dilution of the ingredients. Dilution is required for the generation of concentration graduation which is mandatory for many different assay protocols.

Stochastically reduced communities-Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces.

Microbial community in soil is a complex and dynamic system. Using traditional culture experiments it is difficult to model the stochastic distribution of single organisms of microbial communities in the soil pore's structure. Droplet-based micro-segmented flow technique allows the transfer of the principle of stochastic confinement of stochastically reduced communities from soil micro pores into nanoliter droplets.

Application of micro-segmented flow for two-dimensional characterization of the combinatorial effect of zinc and copper ions on metal-tolerant Streptomyces strains.

The cultivation and growth behavior of metal-tolerant strains of Streptomyce acidiscabies E13 and Streptomyces sp. F4 were studied under droplet-based microfluidics conditions. It was shown that the technique of micro segmented flow is well suited for the investigation of dependence of bacterial growth on different concentrations of either single metal ions or combinations of them.

Stimulation and inhibition of bacterial growth by caffeine dependent on chloramphenicol and a phenolic uncoupler--a ternary toxicity study using microfluid segment technique.

A droplet-based microfluidic technique for the fast generation of three dimensional concentration spaces within nanoliter segments was introduced. The technique was applied for the evaluation of the effect of two selected antibiotic substances on the toxicity and activation of bacterial growth by caffeine. Therefore a three-dimensional concentration space was completely addressed by generating large sequences with about 1150 well separated microdroplets containing 216 different combinations of concentrations.

Uncovering toxicological complexity by multi-dimensional screenings in microsegmented flow: modulation of antibiotic interference by nanoparticles.

The technique of microsegmented flow was applied for the generation of two- and higher dimensional concentration spaces for the screening of toxic effects of selected substances on the bacterium Escherichia coli at the nanolitre scale. Up to about 5000 distinct experiments with different combinations of effector-concentrations could be realized in a single experimental run. This was done with the help of a computer program controlling the flow rates of effector-containing syringe pumps and resulted in the formation of multi-dimensional concentration spaces in segment sequences.

Synergistic effects of metal nanoparticles and a phenolic uncoupler using microdroplet-based two-dimensional approach.

A droplet-based microfluidic technique for testing multiple reagent concentrations is presented. We used this experimental approach to study combined effects of gold (AuNP) and silver nanoparticles (AgNP) with the phenolic uncoupler 2,4-dinitrophenol (DNP) with respect to the growth of Escherichia coli. In order to evaluate the toxicity of binary mixtures, we first encapsulated the E.