An agroecological structure model of compost-soil-plant interactions for sustainable organic farming.

Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.

Effect of radioactive cesium-rich microparticles on radioactive cesium concentration and distribution coefficient in rivers flowing through the watersheds with different contaminated condition in Fukushima.

Radioactive cesium-rich microparticles (CsMPs) derived from the Fukushima Daiichi Nnuclear Power Plant accident were detected from soils and river water around Fukushima Prefecture, Japan. Because CsMPs are insoluble and rich in radioactive cesium (RCs), they may cause the overestimation of solid-water distribution coefficient (Kd) for RCs in the water. Previous studies showed the proportion of RCs derived from CsMPs on RCs concentration in soils collected from areas with different contaminated levels. Because the proportion of RCs concentration derived CsMPs to the RCs concentration of soils in the less contaminated areas is higher than that in the highly contaminated areas, the effect of CsMPs on particulate RCs concentration in river water may be larger in the less contaminated areas. However, the difference in the effects of CsMPs on the particulate RCs concentration and Kd in river water flowing through watersheds with different contaminated levels has not been clarified. In this study, we investigated the effect of CsMPs on the particulate RCs concentration and Kd in two rivers, Takase River and Kami-Oguni River, flowing through the watersheds with different RCs contaminated levels in Fukushima Prefecture. CsMPs might enter rivers due to soil erosion because they were detected only in some samples collected from both rivers during flood events. CsMPs accounted for more than half of particulate RCs concentration in some water samples collected in the flood condition. In particular, the proportion of CsMPs in particulate RCs for the Kami-Oguni River was greater than that for the Takase River. However, when evaluating for the entire water sampling in the flood condition, a proportion of RCs concentration derived from CsMPs in the average RCs concentrations per unit mass of SS in both river waters collected in the flood condition was not large. CsMPs might temporarily increase the particulate RCs concentration and Kd in the flood event, but CsMPs did not significantly affect them when evaluated throughout the event.

Agroecosystem engineering extended from plant-microbe interactions revealed by multi-omics data.

In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approaches in the agroecosystem engineering system, including causal network analysis and predictive modeling.

CESIUM-RICH MICROPARTICLES RUNOFF DURING RAINFALL: A CASE STUDY IN THE TAKASE RIVER.

Cesium-rich microparticles (CsMPs) with high cesium-137 (137Cs) concentrations were released and deposited in surface soil after the Fukushima Daiichi Nuclear Power Plant accident. Radioactive materials on the soil surface layer enter rivers owing to soil erosion during rainfall. In this study, we investigated CsMPs runoff through the river via soil erosion during rainfall in the Takase River watershed in Namie Town, Fukushima Prefecture, Japan. CsMPs were rarely detected in suspended solids (SS) in water samples collected during four rainfalls between February and July 2021. Furthermore, the proportion of 137Cs concentration derived from CsMPs to 137Cs concentration in the form of SS (particulate 137Cs) in the water was ~6% on average, which suggests that 137Cs runoff in the form of CsMPs from the forest to the Takase River was not large.

Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks.

Network-based assessments are important for disentangling complex microbial and microbial-host interactions and can provide the basis for microbial engineering. There is a growing recognition that chemical-mediated interactions are important for the coexistence of microbial species. However, so far, the methods used to infer microbial interactions have been validated with models assuming direct species-species interactions, such as generalized Lotka-Volterra models. Therefore, it is unclear how effective existing approaches are in detecting chemical-mediated interactions. In this paper, we used time series of simulated microbial dynamics to benchmark five major/state-of-the-art methods. We found that only two methods (CCM and LIMITS) were capable of detecting interactions. While LIMITS performed better than CCM, it was less robust to the presence of chemical-mediated interactions, and the presence of trophic competition was essential for the interactions to be detectable. We show that the existence of chemical-mediated interactions among microbial species poses a new challenge to overcome for the development of a network-based understanding of microbiomes and their interactions with hosts and the environment.

Vertical migration of cesium in weathered granite soil under flowing water condition depending on Cs concentration and states of dissolved organic matter.

After the accident at the Fukushima Daiichi nuclear power plant in Japan, the migration of radioactive cesium (Cs) in soils has become a crucial issue since this can negatively affect human health and the surrounding environment. Dissolved organic matter (DOM) may have different influences on Cs migration in soils depending on Cs adsorption sites with different selectivity. It is unclear how DOM affects the rapid migration of Cs in soils under flowing water conditions during rainfall events. This study evaluated the effects of DOM on Cs migration in weathered granite soil depending on Cs adsorption sites by conducting laboratory experiments under different DOM conditions and Cs concentrations in the liquid phase. Cs concentration can affect the fraction of Cs adsorbed onto differently selective sites, and DOM can have different influences on Cs migration in the soil accordingly. Under condition of high-Cs concentration, the DOM adsorbed on the soil reduced Cs migration due to increasing Cs electrostatic adsorption to less selective sites in the soil. Meanwhile, under low-Cs concentration, the DOM adsorbed on the soil enhanced Cs migration because the DOM on the soil decreased the Cs adsorption to highly selective sites. Furthermore, DOM in the liquid phase detached the Cs adsorbed on the less selective sites and enhanced Cs migration in the soil, regardless of the Cs concentration.

Cesium-137 stored on and discharged from banks of an agricultural canal in Iitate, Fukushima.

This study aimed to investigate the dynamics of 137Cs around banks along an agricultural canal for paddy fields in Iitate, Fukushima, Japan. Five plots (2.4-12.6 m2) on the banks were monitored intermittently during six time periods from May 2018 to November 2019. We directly collected runoff water samples discharged from the banks followed by partitioning it into particulate and dissolved fractions and determining 137Cs in them. To investigate the source of 137Cs in the runoff water, we sequentially extracted 137Cs in various chemical forms from litter samples collected on the banks. The results showed that the discharge rates of the dissolved 137Cs per unit area from the plots were lower than those observed at the downstream of the agricultural canal, whereas more than 50% of the 137Cs discharged from the plots was in the dissolved fraction. Moreover, the results indicate that 137Cs stored in the standing plants and the litter was the primary source of the dissolved 137Cs discharged into the agricultural canal. The concentrations of the water-soluble 137Cs in the litter per plot area may have been retained by the sufficiently higher concentrations of 137Cs in litter in other chemical forms and those in the standing plants, which are the source of the litter.

Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield.

Both inorganic fertilizer inputs and crop yields have increased globally, with the concurrent increase in the pollution of water bodies due to nitrogen leaching from soils. Designing agroecosystems that are environmentally friendly is urgently required. Since agroecosystems are highly complex and consist of entangled webs of interactions between plants, microbes, and soils, identifying critical components in crop production remain elusive. To understand the network structure in agroecosystems engineered by several farming methods, including environmentally friendly soil solarization, we utilized a multiomics approach on a field planted with Brassica rapa We found that the soil solarization increased plant shoot biomass irrespective of the type of fertilizer applied. Our multiomics and integrated informatics revealed complex interactions in the agroecosystem showing multiple network modules represented by plant traits heterogeneously associated with soil metabolites, minerals, and microbes. Unexpectedly, we identified soil organic nitrogen induced by soil solarization as one of the key components to increase crop yield. A germ-free plant in vitro assay and a pot experiment using arable soils confirmed that specific organic nitrogen, namely alanine and choline, directly increased plant biomass by acting as a nitrogen source and a biologically active compound. Thus, our study provides evidence at the agroecosystem level that organic nitrogen plays a key role in plant growth.

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community.

Plant roots nurture a wide variety of microbes via exudation of metabolites, shaping the rhizosphere's microbial community. Despite the importance of plant specialized metabolites in the assemblage and function of microbial communities in the rhizosphere, little is known of how far the effects of these metabolites extend through the soil. We employed a fluid model to simulate the spatiotemporal distribution of daidzein, an isoflavone secreted from soybean roots, and validated using soybeans grown in a rhizobox. We then analysed how daidzein affects bacterial communities using soils artificially treated with daidzein. Simulation of daidzein distribution showed that it was only present within a few millimetres of root surfaces. After 14 days in a rhizobox, daidzein was only present within 2 mm of root surfaces. Soils with different concentrations of daidzein showed different community composition, with reduced α-diversity in daidzein-treated soils. Bacterial communities of daidzein-treated soils were closer to those of the soybean rhizosphere than those of bulk soils. This study highlighted the limited distribution of daidzein within a few millimetres of root surfaces and demonstrated a novel role of daidzein in assembling bacterial communities in the rhizosphere by acting as more of a repellant than an attractant.

Effects of the dissolved organic matter on Cs transport in the weathered granite soil.

It is important to understand the migration of Cesium (Cs) in soils, particularly after the nuclear power plant accident at Fukushima Dai-ichi, Japan. Dissolved organic matter (DOM) is one of factors affecting the migration of Cs in soils under flowing water conditions. We investigated the effect of DOM on the migration of Cs adsorbed to the clay planar site via laboratory column experiments. The sequence of DOM application had a significant influence on Cs transport in the soil. When DOM was applied concurrently with or prior to Cs application, the DOM adsorbed on to the clay planar site adsorbed onto the soil solid surface and enhanced Cs adsorption; consequently, it slowed Cs migration in the soil. In particular, in the case of DOM loaded prior to the application of Cs solution, a noticeable delay in Cs migration was observed. On the other hand, when DOM was applied to the soil where the Cs solution had been previously applied, the DOM desorbed Cs from the soil. DOM in liquid phase enhanced the migration of Cs through the formation of binding to organic matter. Majority of Cs affected by DOM was the exchangeable fraction that adsorbed to the clay planar site. In other words, DOM attached to the soil would adsorb Cs as a easily exchangeable form and depress migration of Cs. On the other hand, DOM in the soil solution may up take adsorbed Cs from the soil and enhanced the transport in the form of Cs bound to DOM.

Efficient sampling of shiitake-inoculated oak logs to determine the log-to-mushroom transfer factor of stable cesium.

BACKGROUND: Stable cesium (133Cs) naturally exists in the environment whereas recently deposited radionuclides (e.g., 137Cs) are not at equilibrium. Stable cesium has been used to understand the long-term behavior of radionuclides in plants, trees and mushrooms. We are interested in using 133Cs to predict the future transfer factor (TF) of radiocesium from contaminated logs to shiitake mushrooms in Eastern Japan. However, the current methodology to obtain a representative wood sample for 133Cs analysis involves mechanically breaking and milling the entire log (excluding bark) to a powder prior to analysis. In the current study, we investigated if sawdust obtained from cutting a log along its length at eight points is as robust but a faster alternative to provide a representative wood sample to determine the TF of 133Cs between logs and shiitake. METHODS: Oak logs with ready-to-harvest shiitake fruiting bodies were cut into nine 10-cm discs and each disc was separated into bark, sapwood and heartwood and the concentration of 133Cs was measured in the bark, sapwood, heartwood, sawdust (generated from cutting each disc) and fruiting bodies (collected separately from each disc), and the wood-to-shiitake TF was calculated. RESULTS: We found that the sawdust-to-shiitake TF of 133Cs did not differ (P = 0.223) compared to either the sapwood-to-shiitake TF or heartwood-to-shiitake TF, but bark did have a higher concentration of 133Cs (P < 0.05) compared to sapwood and heartwood. Stable cesium concentration in sawdust and fruiting bodies collected along the length of the logs did not differ (P > 0.05). DISCUSSION: Sawdust can be used as an alternative to determine the log-to-shiitake TF of 133Cs. To satisfy the goals of different studies and professionals, we have described two sampling methodologies (Methods I and II) in this paper. In Method I, a composite of eight sawdust samples collected from a log can be used to provide a representative whole-log sample (i.e., wood and bark), whereas Method II allows for the simultaneous sampling of two sets of sawdust samples-one set representing the whole log and the other representing wood only. Both methodologies can greatly reduce the time required for sample collection and preparation.

Distribution of Radioactive Cesium during Milling and Cooking of Contaminated Buckwheat.

To clarify the behavior of radioactive cesium (Cs) in buckwheat grains during milling and cooking processes, parameters such as processing factor (Pf) and food processing retention factor (Fr) were evaluated in two lots of buckwheat grains, R1 and R2, with different concentrations of radioactive Cs. Three milling fractions, the husk, bran, and flour fractions, were obtained using a mill and electric sieve. The radioactive Cs (134Cs + 137Cs) concentrations in husk and bran were higher than that in grain, whereas the concentration in flour was lower than that in grain. Pf values for the flours of R1 and R2 were 0.60 and 0.80, respectively. Fr values for the flours of R1 and R2 were 0.28 and 0.53, respectively. Raw buckwheat noodles (soba) were prepared using a mixture of buckwheat flour and wheat flour according to the typical recipe and were cooked with boiling water for 0.5, 1, and 2 min, followed by rinsing with water. Pf values for the soba boiled for 2 min (optimal for eating) made with R1 and R2 were 0.34 and 0.40, respectively. Fr values for these R1 and R2 samples were 0.55 and 0.66, respectively. Pf and Fr values for soba boiled for different times for both R1 and R2 were less than 0.6 and 0.8, respectively. Thus, buckwheat flour and its product, soba, cooked by boiling, are considered acceptable for human consumption according to the standard limit for radioactive Cs in buckwheat grains.

Short day length-induced decrease of cesium uptake without altering potassium uptake manner in poplar.

Short day length-induced alteration of potassium (K) localization in perennial trees is believed to be a mechanism for surviving and adapting to severe winters. To investigate the relationship between cesium (Cs) and K localizations, a model tree poplar, hybrid aspen T89, was employed. Under short day length conditions, the amount of 137Cs absorbed through the root and translocated to the root was drastically reduced, but 42K was not. Potassium uptake from the rhizosphere is mediated mainly by KUP/HAK/KT and CNGC transporters. In poplar, however, these genes were constantly expressed under short-day conditions except for a slight increase in the expression a KUP/HAK/KT gene six weeks after the onset of the short-day treatment. These results indicated that the suppression of 137Cs uptake was triggered by short day length but not regulated by competitive Cs+ and K+ transport. We hypothesize that there are separately regulated Cs+ and K+ transport systems in poplar.

Inspections of radiocesium concentration levels in rice from Fukushima Prefecture after the Fukushima Dai-ichi Nuclear Power Plant accident.

We summarize the inspections of radiocesium concentration levels in rice produced in Fukushima Prefecture, Japan, for 3 years from the nuclear accident in 2011. In 2011, three types of verifications, preliminary survey, main inspection, and emergency survey, revealed that rice with radiocesium concentration levels over 500 Bq/kg (the provisional regulation level until March 2012 in Japan) was identified in the areas north and west of the Fukushima nuclear power plant. The internal exposure of an average adult eating rice grown in the area north of the nuclear plant was estimated as 0.05 mSv/year. In 2012, Fukushima Prefecture authorities decided to investigate the radiocesium concentration levels in all rice using custom-made belt conveyor testers. Notably, rice with radiocesium concentration levels over 100 Bq/kg (the new standard since April 2012 in Japan) were detected in only 71 and 28 bags out of the total 10,338,000 in 2012 and 11,001,000 in 2013, respectively. We considered that there were almost no rice exceeding 100 Bq/kg produced in Fukushima Prefecture after 3 years from the nuclear accident, and the safety of Fukushima's rice were ensured because of the investigation of all rice.

Removal of radioactive Cs from gravel conglomerate using water containing air bubbles.

Remediation of sites contaminated with radioactive material such as Cs is important because of the risk posed to human health. Here, we report the effectiveness of water containing air bubbles with a diameter around 100 nm (nanobubbled water, NB water) for the removal of radioactive Cs. Laboratory experiments confirmed that NB water is more effective than purified water and as effective as water with neutral detergent in the removal of Cs-137 from gravel. Moreover, NB water retains its effectiveness even after storage for 7 d. Finally, NB water produced onsite from tap water was found to be effective for removal of radioactive Cs from gravel conglomerate in Fukushima, Japan.

An aluminum influence on root circumnutation in dark revealed by a new super-HARP (high-gain avalanche rushing amorphous photoconductor) camera.

The circumnutation of a rice root under dark conditions was observed using a highly sensitive camera, a new super-HARP camera. A rice root showed regular rhythmic movement with fixed angle. When treated with Al (5 microM AlCl3), the rotation angle of the root tip was drastically decreased and then the movement was resumed again, whereas the root elongation rate was constant. With the increase of Al concentration, the cycle-fading period became shorter. This is the first report to show that an Al treatment ceased the rotation movement of the root but not elongation.