Degradation and half-life of DNA present in biomass from a genetically-modified organism during land application

Multi 'omic data integration: A review of concepts, considerations, and approaches

The application of 'omic techniques including, but not limited to genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, and metabolomics to generate multiple datasets from a single sample have facilitated hypothesis generation leading to the identification of biological, molecular and ecological functions and mechanisms, as well as associations and correlations. Despite their power and promise, a variety of challenges must be considered in the successful design and execution of a multi-omics study. In this review, various 'omic technologies applicable to single- and meta-organisms (i.e., host + microbiome) are described, and considerations for sample collection, storage and processing prior to data generation and analysis, as well as approaches to data storage, dissemination and analysis are discussed. Finally, case studies are included as examples of multi-omic applications providing novel insights and a more holistic understanding of biological processes.

A mirror-image protein-based information barcoding and storage technology

A mirror-image protein-based information barcoding and storage technology wherein D-amino acids are used to encode information into mirror-image proteins that are chemically synthesized is described. These mirror-image proteins were then fused into various materials from which information-encoded objects were produced. Subsequently, the mirror-image proteins were extracted from the objects using biotin-streptavidin resin-mediated specific enrichment and cleaved using an Ni(II)-mediated selective peptide cleavage. Protein sequencing was accomplished using liquid chromatography/tandem mass spectrometry (LC-MS/MS) and then transcoded into the recorded information. We demonstrated the use of this technology to encode Chinese words into mirror-image proteins, which were then fused onto a poly(ethylene terephthalate) (PET) film and retrieved and decoded by LC-MS/MS sequencing. Compared to information barcoding and storage technologies using natural biopolymers, the mirror-image biopolymers used in our technology may be more stable and durable.

Ecotoxicological Assessment of DNA-Tagged Silica Particles for Environmental Tracing

Environmental tracers are chemical species that move with a fluid and allow us to understand its origin and material transport properties. DNA-based materials have been proposed and used for tracing due to their potential for multitracing with high specificity and sensitivity. For large-scale applications of this new material it is of interest to understand its impact on the environment. We therefore assessed the ecotoxicity of sub-micron silica particles with and without encapsulated DNA in the context of surface and underground tracing of natural waterflows using standard ecotoxicity assays according to ISO standards. Acute toxicity tests were performed with Daphnia magna (48 h), showing no effect on mobility at tracer concentrations below 300 ppm. Chronic ecotoxicological potential was tested with Raphidocelis subcapitata (green algae) (72 h) and Ceriodaphnia species (7 d) with no effect observed at realistic exposure scenario concentrations for both silica particles with and without encapsulated DNA. These results suggest that large-scale environmental tracing with DNA-tagged silica particles in the given exposure scenarios has a low impact on aquatic species with low trophic levels such as select algae and planktonic crustaceans.

Organic farming practices utilizing spent microbial biomass from an industrial fermentation facility promote transition to copiotrophic soil communities

Organic farming has become more prevalent in recent years as consumer demand for organic food and fiber has rapidly grown. Until recently, organic fertilizers and soil amendments have largely been based on the practices of returning crop residues, manures and related agricultural wastes back to crop production areas. One rapidly growing segment in commercial organic fertilizer development is the use of spent microbial biomass (SMB) from industrial fermentation processes. While SMB is widely accepted in many organic farming systems (OFS), little is known concerning the effectiveness, environmental impact, and influence on prokaryotic communities in soils receiving this treatment. In this study, a comparative analysis of bacterial communities associated with OFS and conventional farming systems was performed over a growing season for a field containing yellow dent corn (Zea mays). A statistically significant increase in microbial population α-diversity, along with a strong recruitment of Proteobacteria and Actinobacteria populations, was observed in soils treated with SMB when compared to areas in the field that utilized conventional farmer practices. These phyla are members of the copiotrophic subgroup, and considered a signature for the use of traditional organic fertilizers. These results provide valuable new information that SMB functions similarly to traditional organic fertilizers in promoting a high level of functional prokaryotic diversity and plant growth-promoting bacteria, but in contrast do not contribute directly to viable microorganisms in the soil due to the sterilization of SMB prior to land application.

Silica-Encapsulated DNA-Based Tracers for Aquifer Characterization

Environmental tracing is a direct way to characterize aquifers, evaluate the solute transfer parameter in underground reservoirs, and track contamination. By performing multitracer tests, and translating the tracer breakthrough times into tomographic maps, key parameters such as a reservoir's effective porosity and permeability field may be obtained. DNA, with its modular design, allows the generation of a virtually unlimited number of distinguishable tracers. To overcome the insufficient DNA stability due to microbial activity, heat, and chemical stress, we present a method to encapsulated DNA into silica with control over the particle size. The reliability of DNA quantification is improved by the sample preservation with NaN₃ and particle redispersion strategies. In both sand column and unconsolidated aquifer experiments, DNA-based particle tracers exhibited slightly earlier and sharper breakthrough than the traditional solute tracer uranine. The reason behind this observation is the size exclusion effect, whereby larger tracer particles are excluded from small pores, and are therefore transported with higher average velocity, which is pore size-dependent. Identical surface properties, and thus flow behavior, makes the new material an attractive tracer to characterize sandy groundwater reservoirs or to track multiple sources of contaminants with high spatial resolution.