Nucleic Acid Aptamers for Pesticides, Toxins, and Biomarkers in Agriculture

Nucleic acid aptamers are short single-stranded DNA/RNA (ssDNA/RNA) oligonucleotides that can selectively bind to the targets. They are widely used in medicine, biosensing, and diagnostic assay. They have also been identified and extensively used for various targets in agriculture. In this review we summarize the progress of nucleic acid aptamers on pesticides (herbicides, insecticides, and fungicides), toxins, specific biomarkers of crops, and plant growth regulators in agricultural field in recent years. The basic process of aptamer selection, the already identified DNA/RNA aptamers and the aptasensors are discussed. We also discuss the future perspectives and the challenges for aptamer development in agriculture.

Selection of DNA Aptamers for Root Exudate l-Serine Using Multiple Selection Strategies

Agricultural biosensing can aid decisions about crop health and maintenance, because crops release root exudates that can inform about their status. l-Serine has been found to be indicative of nitrogen uptake in wheat and canola. The development of a biosensor for l-serine could allow farmers to monitor crop nutrient demands more precisely. The development of robust l-serine-binding DNA aptamers is described. Because small molecules can be challenging targets for Systematic Evolution of Ligands by EXponential enrichment (SELEX), three separate DNA libraries were used for SELEX experiments. A l-homocysteine aptamer was randomized to create a starting library for a l-serine selection (randomized SELEX). The final selection rounds of the l-homocysteine selection were also used as a starting library for l-serine (redirected SELEX). Finally, an original DNA library was used (original SELEX). All three SELEX experiments produced l-serine-binding aptamers with micromolar affinity, with Red.1 aptamer having a K_d of 7.9 ± 3.6 μM. Truncation improved the binding affinity to 5.2 ± 2.7 μM, and from this sequence, a Spiegelmer with improved nuclease resistance was created with a K_d of 2.0 ± 0.8 μM. This l-serine-binding Spiegelmer has the affinity and stability to be incorporated into aptamer-based biosensors for agricultural applications.

Responses of rhizosphere soil bacteria to 2-year tillage rotation treatments during fallow period in semiarid southeastern Loess Plateau

BACKGROUND

Soil compaction can be mitigated by deep tillage and subsoiling practices following a long period of no-tillage. Fallow tillage rotation methods are frequently used to improve water availability in the soils of the southeastern Loess Plateau region of China. Rhizosphere soil bacteria are ecologically important for the transformation of matter and energy in the plant root system and can be influenced by tillage rotation treatments. However, the effect of tillage rotations on the bacterial community and structure of rhizosphere soil is not well understood.

METHODS

A two-year field experiment was conducted with four tillage rotation treatments, including subsoil-subsoil (SS-SS), subsoil-deep tillage (SS-DT), deep tillage-deep tillage (DT-DT), and the control treatment of no-tillage-no-tillage (NT-NT). Our study was conducted during wheat's fallow period to investigate the abundance, diversity, and functions of rhizosphere soil bacteria using high-throughput sequencing technology.

RESULTS

Our results showed that tillage rotation methods significantly influenced the bacterial diversity and composition of the rhizosphere soil in the plough layer (20-40 cm depth) by altering the moisture content of the soil. The metabolism, environmental information processing, and genetic information processing of the bacteria in the rhizosphere soil were affected. The most abundant phyla across all samples were Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Bacteroidetes, Gemmatimonadetes, Frimicutes, Chloroflexi, Nitrospirae, and Verrucomicrobia, which are classic bacterial decomposers in soil. The bacterial diversity and composition was similar for treatments causing higher soil perturbation (SS-DT and DT-DT), which disrupted the balance between aerobic and anaerobic bacteria. The less disruptive tillage methods (SS-SS and NT-NT), preserved the integrity of the soil bacteria. However, the NT-NT treatment may have led to soil compaction, particularly in the 20-40 cm layer. These results suggested that SS-SS was the most effective tillage rotation practice to accumulate soil moisture, maintain the balance between aerobic and anaerobic bacteria, and to enhance the metabolic capacity of rhizosphere soil bacteria. This method may have a significant impact on the sustainable development and farming practices of dryland agriculture.

Metabolomics: A Way Forward for Crop Improvement

Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.

Personalized Medicine for Crops? Opportunities for the Application of Molecular Recognition in Agriculture

This perspective examines the detection of rhizosphere biomarkers, namely, root exudates and microbial metabolites, using molecular recognition elements, such as molecularly imprinted polymers, antibodies, and aptamers. Tracking these compounds in the rhizosphere could provide valuable insight into the status of the crop and soil in a highly localized way. The outlook and potential impact of the combination of molecular recognition and other innovations, such as nanotechnology and precision agriculture, and the comparison to advances in personalized medicine are considered.