Application Potentials of Geobiotechnology in Mining, Mineral Processing, and Metal Recycling.

This chapter highlights the huge and manifold possibilities of reactions which result from the interactions between microorganisms and the geosphere and which are used for mining, mineral processing, and metal recycling. Besides the introduction (Sect. 1) the contribution is divided into five different sections describing the mobilization (Sect. 2) and immobilization (Sect. 3) of valuable substances, the processes of biosorption and bioaccumulation (Sect. 4), as well as transformation of metals into metal organic compounds (Sect. 5). A special topic (Sect. 6) addresses the application of CO2 as an important component for the formation of energy-rich compounds and chemicals. Each section starts with an overview of the relevant reactions and an explanation of the reaction condition. Afterward information about applications and different technological processes as well as sustainability aspects are provided. Graphical Abstract.

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics.

We propose a joint experimental and theoretical approach to the automated reconstruction of elemental fluxes in microbial communities. While stable isotope probing of proteins (protein-SIP) has been successfully applied to study interactions and elemental carbon and nitrogen fluxes, the volume and complexity of mass spectrometric data in protein-SIP experiments pose new challenges for data analysis. Together with a flexible experimental setup, the novel bioinformatics tool MetaProSIP offers an automated high-throughput solution for a wide range of (13)C or (15)N protein-SIP experiments with special emphasis on the analysis of metaproteomic experiments where differential labeling of organisms can occur. The information calculated in MetaProSIP includes the determination of multiple relative isotopic abundances, the labeling ratio between old and new synthesized proteins, and the shape of the isotopic distribution. These parameters define the metabolic capacities and dynamics within the investigated microbial culture. MetaProSIP features a high degree of reproducibility, reliability, and quality control reporting. The ability to embed into the OpenMS framework allows for flexible construction of custom-tailored workflows. Software and documentation are available under an open-source license at www.openms.de/MetaProSIP.

StyA1 and StyA2B from Rhodococcus opacus 1CP: a multifunctional styrene monooxygenase system.

Two-component flavoprotein monooxygenases are emerging biocatalysts that generally consist of a monooxygenase and a reductase component. Here we show that Rhodococcus opacus 1CP encodes a multifunctional enantioselective flavoprotein monooxygenase system composed of a single styrene monooxygenase (SMO) (StyA1) and another styrene monooxygenase fused to an NADH-flavin oxidoreductase (StyA2B). StyA1 and StyA2B convert styrene and chemical analogues to the corresponding epoxides at the expense of FADH2 provided from StyA2B. The StyA1/StyA2B system presents the highest monooxygenase activity in an equimolar ratio of StyA1 and StyA2B, indicating (transient) protein complex formation. StyA1 is also active when FADH2 is supplied by StyB from Pseudomonas sp. VLB120 or PheA2 from Rhodococcus opacus 1CP. However, in both cases the reductase produces an excess of FADH2, resulting in a high waste of NADH. The epoxidation rate of StyA1 heavily depends on the type of reductase. This supports that the FADH2-induced activation of StyA1 requires interprotein communication. We conclude that the StyA1/StyA2B system represents a novel type of multifunctional flavoprotein monooxygenase. Its unique mechanism of cofactor utilization provides new opportunities for biotechnological applications and is highly relevant from a structural and evolutionary point of view.