Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions

Challenges in imaging and predictive modeling of rhizosphere processes

Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes

Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy

In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.Web of Science9art. no. e5254

Turning gold into 'junk': transposable elements utilize central proteins of cellular networks

The numerous discovered cases of domesticated transposable element (TE) proteins led to the recognition that TEs are a significant source of evolutionary innovation. However, much less is known about the reverse process, whether and to what degree the evolution of TEs is influenced by the genome of their hosts. We addressed this issue by searching for cases of incorporation of host genes into the sequence of TEs and examined the systems-level properties of these genes using the Saccharomyces cerevisiae and Drosophila melanogaster genomes. We identified 51 cases where the evolutionary scenario was the incorporation of a host gene fragment into a TE consensus sequence, and we show that both the yeast and fly homologues of the incorporated protein sequences have central positions in the cellular networks. An analysis of selective pressure (Ka/Ks ratio) detected significant selection in 37% of the cases. Recent research on retrovirus-host interactions shows that virus proteins preferentially target hubs of the host interaction networks enabling them to take over the host cell using only a few proteins. We propose that TEs face a similar evolutionary pressure to evolve proteins with high interacting capacities and take some of the necessary protein domains directly from their hosts

Report from the 5th international symposium on mycotoxins and toxigenic moulds : challenges and perspectives (MYTOX) held in Ghent, Belgium, May 2016

The association research platform MYTOX “Mycotoxins and Toxigenic Moulds” held the 5th meeting of its International Symposium in Ghent, Belgium on 11 May 2016.[...

Vision-based weed identification with farm robots

Robots in agriculture offer new opportunities for real time weed identification and quick removal operations. Weed identification and control remains one of the most challenging task in agriculture, particularly in organic agriculture practices. Considering environmental impacts and food quality, the excess use of chemicals in agriculture for controlling weeds and diseases is decreasing. The cost of herbercides and their field applications must be optimized. As an alternative, a smart weed identification technique followed by the mechanical and thermal weed control can fulfill the organic farmers’ expectations. The smart identification technique works on the concept of ‘shape matching’ and ‘active shape modeling’ of plant and weed leafs. The automated weed detection and control system consists of three major tools. Such as: i) eXcite multispectral camera, ii) LTI image processing library and iii) Hortibot robotic vehicle. The components are combined in Linux interface environment in the eXcite camera associate PC. The laboratory experiments for active shape matching have shown interesting results which will be further enhanced to develop the automated weed detection system. The Hortibot robot will be mounted with the camera unit in the front-end and the mechanical weed remover in the rear-end. The system will be upgraded for intense commercial applications in maize and other row crops

Decomposing Dual Scale Soil Surface Roughness for Microwave Remote Sensing Applications

Soil surface roughness, as investigated in this study, is decomposed in a dual scale process. Therefore, we investigated photogrammetrically acquired roughness information over different agricultural fields in the size of 6-22 m(2) and decomposed them into a dual scale process by using geostatistical techniques. For the characterization of soil surface roughness, we calculated two different roughness indices (the RMS height s and the autocorrelation length l) differing significantly for each scale. While we could relate the small scale roughness pattern clearly to the seedbed rows, the larger second scale pattern could be related to the appearance of wheel tracks of the tillage machine used. As a result, major progress was made in the understanding of the different scales in soil surface roughness characterization and its quantification possibilities