Development of a novel and rapid phenotype-based screening method to assess rice seedling growth

Background: Rice (Oryza sativa) is one of the most important model crops in plant research. Despite its considerable advantages, (phenotypic) bioassays for rice are not as well developed as for Arabidopsis thaliana. Here, we present a phenotype-based screening method to study shoot-related parameters of rice seedlings via an automated computer analysis. Results: The phenotype-based screening method was validated by testing several compounds in pharmacological experiments that interfered with hormone homeostasis, confirming that the assay was consistent with regard to the anticipated plant growth regulation and revealing the robustness of the set-up in terms of reproducibility. Moreover, abiotic stress tests using NaCl and DCMU, an electron transport blocker during the light dependent reactions of photosynthesis, confirmed the validity of the new method for a wide range of applications. Next, this method was used to screen the impact of semi-purified fractions of marine invertebrates on the initial stages of rice seedling growth. Certain fractions clearly stimulated growth, whereas others inhibited it, especially in the root, illustrating the possible applications of this novel, robust, and fast phenotype-based screening method for rice. Conclusions: The validated phenotype-based and cost-efficient screening method allows a quick and proper analysis of shoot growth and requires only small volumes of compounds and media. As a result, this method could potentially be used for a whole range of applications, ranging from discovery of novel biostimulants, plant growth regulators, and plant growth-promoting bacteria to analysis of CRISPR knockouts, molecular plant breeding, genome-wide association, and phytotoxicity studies. The assay system described here can contribute to a better understanding of plant development in general

It takes three to tango: citizen, fundamental and applied science

Citizen science is an undervalued tool in a scientist's toolbox with the potential to go beyond primary data collection to strengthen fundamental and applied science. We call for the integration of these three disciplines to make agriculture sustainable and adaptive to climate change, with North-Western European soybean cultivation as showcase

Citizen science boosts fundamental and applied research for sustainable soybean cultivation in North‐Western Europe

Societal Impact Statement To help save our planet, we need to shift to plant‐based protein food and enhance sustainable agricultural practices. Cultivation of legumes, including soybean, will be key because they produce protein‐rich beans without high applied fertilizer input. This complex challenge involves many stakeholders beyond the agricultural sector. In the ‘Soy in 1000 Gardens’ project, we engaged more than thousand citizens in a 6‐month gardening project aiming at facilitating sustainable soybean cultivation in Belgium. Our work shows that with the right approach, citizen science can provide insights to develop more sustainable agri‐food systems when integrated with fundamental and applied science. Summary The global food system faces numerous challenges in its pursuit of sustainability. Shifting to more plant‐based protein sources as well as transitioning to self‐reliant agri‐food systems is one way to meet these challenges. This transition requires the involvement of multiple stakeholders beyond the agricultural sector such as the citizens themselves. In this study, we employed a citizen science approach through the ‘Soy in 1000 Gardens’ project, which engaged more than 1000 citizen scientists in a 6‐month gardening project during which citizens not only observed plant growth but also executed plant growth measurements that meet scientific standards. We aimed at increasing the awareness about the power of soybean and its symbionts for sustainable plant protein production and at isolating efficient nitrogen‐fixing rhizobia to be used by local farmers to produce protein‐rich soybeans. The results suggest that the success of citizen science projects depends on the level of engagement and the provision of adequate support, among other factors. This study thus highlights the potential of citizen science to address complex challenges and contribute to more sustainable agri‐food systems when properly integrated. Unique in its scope, the project provided important insights into the drivers of participation, attrition and data quality

Opposing effects of trans‐ and cis‐cinnamic acid during rice coleoptile elongation

Abstract The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a trans‐ or cis‐form. In contrast to the proven bioactivity of the cis‐form (c‐CA), the activity of trans‐CA (t‐CA) is still a matter of debate. We tested both compounds using a submerged rice coleoptile assay and demonstrated that they have opposite effects on cell elongation. Notably, in the tip of rice coleoptile t‐CA showed an inhibiting and c‐CA a stimulating activity. By combining transcriptomics and (untargeted) metabolomics with activity assays and genetic and pharmacological experiments, we aimed to explain the underlying mechanistic processes. We propose a model in which c‐CA treatment activates proton pumps and stimulates acidification of the apoplast, which in turn leads to the loosening of the cell wall, necessary for elongation. We hypothesize that c‐CA also inactivates auxin efflux transporters, which might cause a local auxin accumulation in the tip of the coleoptile. For t‐CA, the phenotype can partially be explained by a stimulation of cell wall polysaccharide feruloylation, leading to a more rigid cell wall. Metabolite profiling also demonstrated that salicylic acid (SA) derivatives are increased upon t‐CA treatment. As SA is a known antagonist of auxin, the shift in SA homeostasis provides an additional explanation of the observed t‐CA‐mediated restriction on cell growth

Opposing effects of trans- and cis‐cinnamic acid during rice coleoptile elongation

The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a trans- or cis-form. In contrast to the proven bioactivity of the cis-form (c-CA), the activity of trans-CA (t-CA) is still a matter of debate. We tested both compounds using a submerged rice coleoptile assay and demonstrated that they have opposite effects on cell elongation. Notably, in the tip of rice coleoptile t-CA showed an inhibiting and c-CA a stimulating activity. By combining transcriptomics and (untargeted) metabolomics with activity assays and genetic and pharmacological experiments, we aimed to explain the underlying mechanistic processes. We propose a model in which c-CA treatment activates proton pumps and stimulates acidification of the apoplast, which in turn leads to the loosening of the cell wall, necessary for elongation. We hypothesize that c-CA also inactivates auxin efflux transporters, which might cause a local auxin accumulation in the tip of the coleoptile. For t-CA, the phenotype can partially be explained by a stimulation of cell wall polysaccharide feruloylation, leading to a more rigid cell wall. Metabolite profiling also demonstrated that salicylic acid (SA) derivatives are increased upon t-CA treatment. As SA is a known antagonist of auxin, the shift in SA homeostasis provides an additional explanation of the observed t-CA-mediated restriction on cell growth

Flemish soils contain rhizobia partners for Northwestern Europe‐adapted soybean cultivars

In Europe, soybean (Glycine max) used for food and feed has to be imported, causing negative socioeconomic and environmental impacts. To increase the local production, breeding generated varieties that grow in colder climates, but the yield using the commercial inoculants is not satisfactory in Belgium because of variable nodulation efficiencies. To look for indigenous nodulating strains possibly adapted to the local environment, we initiated a nodulation trap by growing early-maturing cultivars under natural and greenhouse conditions in 107 garden soils in Flanders. Nodules occurred in 18 and 21 soils in the garden and greenhouse experiments respectively. By combining 16S rRNA PCR on single isolates with HiSeq 16S metabarcoding on nodules, we found a large bacterial richness and diversity from different soils. Furthermore, using Oxford Nanopore Technologies sequencing of DNA from one nodule, we retrieved the entire genome of a Bradyrhizobium species, not previously isolated, but profusely present in that nodule. These data highlight the need of combining diverse identification techniques to capture the true nodule rhizobial community. Eight selected rhizobial isolates were subdivided by whole-genome analysis in three genera containing six genetically distinct species that, except for two, aligned with known type strains and were all able to nodulate soybean in the laboratory

A novel role for the transcription factor HIF-1α in the formation of mast cell extracellular traps.

MCs (mast cells) are critical components of the host innate immune defence against bacterial pathogens, providing a variety of intra- and extra-cellular antimicrobial functions. In the present study we show, for the first time, that the transcriptional regulator HIF-1α (hypoxia-inducible factor-1α) mediates the extracellular antimicrobial activity of human and murine MCs by increasing the formation of MCETs (MC extracellular traps)