Understanding how microbial communities assemble is central to predicting ecosystem function. Although predators strongly influence bacterial communities through predation, the role of microbial predators in modulating global microbial divergence and convergence patterns remains largely neglected. Here, we integrated global-scale amplicon sequencing data, controlled field experiments, and reconstructions of natural and synthetic communities to examine predator-mediated community assembly mechanisms. We show that bacterivorous protists exert dual, scale-dependent effects on microbial communities: promoting local convergence by suppressing dominant bacterial taxa, while generating global divergence through species-specific predation effects. We find that predator identity and prey susceptibility jointly determine convergence outcomes. Communities dominated by predator-resistant taxa exhibit reduced convergence under predation pressure, revealing a predictable trait-based filtering mechanism. This work establishes bacterivorous protists as key, context-dependent agents of biogeography and suggests new opportunities for microbiome engineering, where targeted use of protists may steer microbial communities toward functional configurations that enhance soil health and ecosystem resilience.

Salinity tolerance in rice is a multilevel trait integrating ion and ROS homeostasis, tissue tolerance, and whole-plant physiology; future breeding requires combining omics-guided selection, genome editing, and field-relevant phenotyping. Salinity stress is one of the extreme abiotic stress factors that reduces rice yield (Oryza sativa L.) and affects about 20

Global warming and associated environmental changes are reducing arable land and intensifying salinization risks, posing growing threats to food security. Soil salinity is an increasing threat to agricultural productivity worldwide, particularly in arid and semi-arid areas. Wheat (Triticum aestivum L.) is one of the most important and widely cultivated cereal crops for human consumption and livestock feed. However, with increasing water scarcity and the incidence of salt-affected lands, wheat productivity is increasingly affected by salinity. Previous studies have investigated salinity tolerance mechanisms mainly at the seedling and reproductive stages of wheat; however, comparatively fewer studies integrate rapid biochemical and physiological responses during the first hours of germination stress exposure together with transcriptional analyses during early seedling establishment, even though this stage is critical for stand establishment. Here, we evaluated early physiological and transcriptional responses of salt-tolerant, moderate, and sensitive wheat cultivars exposed to 0 or 150 mM NaCl during germination and the early seedling stage. Tolerant and sensitive cultivars showed contrasting germination performance under salinity. Physiological analysis showed that salt-tolerant cultivars exhibited higher proline accumulation and higher antioxidant enzyme activities (CAT, SOD, and GR), while maintaining lower MDA levels under salinity compared with sensitive cultivars. Notably, tolerant cultivars showed marked upregulation of TaHKT1;4, TaP5CS, TaMYB, and TaDHN genes associated with ion homeostasis, osmoprotectant metabolism, and stress-responsive regulation. These responses represent integrated early-stage biochemical, physiological, and transcriptional indicators of salinity responsiveness rather than direct predictors of final yield performance.

Salinity is a severe environmental stressor that reduces crop performance, alters soil microbial communities, and influences greenhouse gas emissions such as methane (CH4). Climate change is expected to further increase salinity globally. Although plants have evolved physiological and molecular mechanisms to cope with salinity, the role of plant-microbiome interactions in salinity tolerance and their link to CH4 emissions remain poorly understood. Here, we investigated the interactions among plant salinity tolerance, rhizobiome, and CH4 emission under salinity stress. We used salt-tolerant and salt-sensitive rice genotypes grown in nutrient-poor paddy field soil and nutrient-rich commercial nursery soil under climate-controlled greenhouse conditions with salinity stress until harvesting. Salt-sensitive genotypes exhibited decreases in early biomass and gas exchange due to salinity stress under nutrient-rich nursery soil. However, salinity effects were mitigated by plant-microbiome interactions, which improved plant growth performance. Rhizosphere microbiome analysis revealed that Rhizobacteria, including Cyanobacteria, were associated with plant development and salinity tolerance. Salinity altered methanogenic archaeal communities, especially Methanobacteria and Methanocellia, with salt-tolerant genotypes releasing more CH4 during stress. Gas exchange and antioxidant enzyme activity were positively correlated with CH4 emissions, suggesting an association between improved physiological performance under salinity and microbial methanogenesis. Gene expression profiling revealed a significant upregulation of hormone- and ion-transport-related genes in paddy soil, which may be associated with stress tolerance, microbial activity, and CH4 emissions. This study proposes a mechanistic framework that links plant salinity tolerance, rhizosphere microbial dynamics, and methane production, illustrating how these interconnected processes shape plant performance and the environmental outcomes. These findings emphasize the necessity of balancing agricultural productivity with CH4 emissions and soil resilience under climate-induced stress.

Maternally inherited extranuclear genomes (ptDNA and mtDNA) and epigenetic mechanisms are known to affect offspring phenotypes; nevertheless, their integrated function in stress adaptation remains incompletely understood. Classical breeding strategies have mostly ignored these non-Mendelian influences by focusing exclusively on nuclear genome inheritance. We developed reciprocal rice hybrids from selected salt-tolerant and salt-sensitive progenitors and utilized a multi-omics strategy-comprising whole-genome sequencing, WGS-derived cytosine content profiling, transcriptomics, and phenotypic evaluations-to understand the maternal contribution to salinity tolerance of rice offspring. Despite sharing a broadly biparental nuclear genetic background, maternal-tolerant rice hybrids demonstrated improved performance, including better growth, photosynthesis, ion homeostasis, and yield relative to maternal-sensitive rice hybrids under salinity stress. Organellar genome sequencing revealed predominantly maternal inheritance. Cytosine profiling indicated CpG and CHG content similarity to the maternal genotype. Transcriptomic data revealed maternal-aligned expression of stress-responsive and organelle-associated genes, consistent with enhanced performance in maternal-tolerant hybrids. Our results from a multi-omics approach support a strong association between maternal cytoplasmic inheritance and differential stress responses in rice hybrids. This non-Mendelian model of stress tolerance, informed by multi-omics integration, provides innovative insights into maternal regulation of stress resilience in rice and proposes an effective strategy for breeding salt-tolerant crops in climate-challenged areas.

Salinity is one of the severe abiotic stress factors that affect approximately 50% of planted and irrigated agricultural fields. The determination of plant response to salinity is the key factor that reduces yield lost in crop production. Transgenerational plasticity is a nongenetic modification that provides a mechanism for plants to "remember" and adapt to environmental conditions experienced by their ancestors, contributing to the phenotypic plasticity and resilience of plant populations over successive generations. This ability to retain stress memory enables plants to respond more effectively to recurring salinity stress, potentially enhancing crop adaptation and productivity. The determination of transgenerational plasticity of salinity tolerance has some key research elements that can be focused on heritable modifications. In this chapter, we explain the methods of transgenerational plasticity of salinity tolerance research.

Salinity is a major abiotic stress that threatens global food security, particularly in arid and semi-arid regions. Rice (Oryza sativa L.) is a stable food for over half of the world's population. Rising soil salinity, driven by climate change and unsustainable irrigation practices, is expected to affect nearly half of the world's arable lands by 2050. This review focuses on the role of the hst1 gene, a mutant form of OsRR22, in enhancing salinity tolerance in rice. The hst1 gene plays a crucial role in maintaining ion homeostasis, scavenging reactive oxygen species (ROS), and regulating stress-responsive signaling pathways, all of which are critical for mitigating salt-induced damage in rice. Under salt stress, the hst1 mutation enables rice plants to accumulate less sodium (Na+) and more potassium (K+), thus preserving cellular function and enhancing photosynthetic efficiency. Additionally, hst1 activates antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR), which protect cells from oxidative damage caused by ROS. The gene also modulates transcription factors that regulate downstream stress-response genes, contributing to improved growth and yield under saline conditions. By understanding the physiological and molecular mechanisms underlying hst1-mediated salt tolerance, this review provides insights into breeding strategies for developing salt-tolerant rice varieties. Such advancements are essential for sustaining rice production in saline-affected regions and ensuring global food security in the face of climate change and population growth.

Salinity is one of the most destructive abiotic stresses limiting rice productivity worldwide. The present study investigates the role of the native soil microbiome in enhancing salinity tolerance of the salt-sensitive Oryza sativa ssp. japonica cv. Nipponbare. Plants were grown under control (0 mM NaCl) and salinity (75 mM NaCl) conditions with microbiome presence (Mb⁺) or absence (Mb⁻). Growth parameters, pigment composition, and gas-exchange traits were quantified, followed by correlation, random forest, and principal component analyses. Salinity stress markedly suppressed plant height, biomass, chlorophyll content, and photosynthetic rate, whereas microbiome inoculation significantly alleviated these effects. Under salinity, Mb⁺ plants exhibited higher plant height, chlorophyll a+b, β-carotene, net photosynthetic rate (Aₙ), and stomatal conductance (gₛ) compared with Mb⁻ plants. Correlation and machine-learning analyses identified Aₙ and chlorophyll a as the most important predictors of microbiome-associated salinity tolerance in rice. Multivariate clustering revealed that Mb⁺ plants under salinity displayed physiological profiles similar to non-stressed controls, suggesting microbiome-mediated buffering of stress responses. Overall, the results indicate that the native soil microbiome enhances photosynthetic resilience and biomass accumulation under salinity, offering a sustainable biological approach to improve rice performance in salt-affected soils.

The authors would like to make the following corrections to the published paper [...]

One of the most important climate change-related issues that has extremely negative impacts on terrestrial life is soil salinization, especially in lowland paddy fields. Despite the enormous impact of salinity on microbial life, the majority of research focused on bacteria and fungi, neglecting the vast majority of eukaryotic diversity, the protists. Here we aimed to understand the sole impact of the soil salinity on protist communities in paddy field soil. To exclude the variations in other environmental factors that co-varies with the soil EC, we conducted a controlled in vitro experiment to study the direct effect of gradually increased salinity levels (ranging from 0.1 dS m-1 to 12 dS m-1) on protists in three non-saline (<0.3 dS m-1) paddy field soils. Then, our in vitro results were confirmed in a field study, in which seawater intrusion caused the accumulation of sea salts in paddy fields along a river. The results of the in vitro and field studies were consistent, showing that alpha and beta diversities of protists are affected by soil salinity. While protist alpha diversity exhibited inconsistent patterns across soil types, beta diversity showed strong and consistent clustering by the salinity gradient. Although salinity significantly shifted protist communities and caused a 10-fold decrease in 18S rRNA gene abundances of protists, protists maintained functional stability, suggesting that even with the compositional shifts, the critical ecosystem functions, such as predation and primary production, remained intact. These results underscore the importance of functional redundancy in sustaining ecosystem functions under salinity stress.

To achieve global goals for sustainable development, such as zero hunger and ensuring food security, the effect of climate change on plant production and overcoming decreasing crop yields caused by environmental stress factors must be understood. Soil salinity is a serious environmental stress factor that threatens food security, combined with global warming, reduced arable land, and the growing human population. Seven percent of the total soil areas of the world are affected by salt, which represents 33% of agricultural land. These areas are getting increased due to unplanned irrigation and aridity. It is reported that 50% of the cultivation areas will be destroyed in 25 years, depending on increased salinity. One of the promising solutions is salt stress-tolerant plant breeding to improve crop yield and quality. Currently, conventional breeding strategies are increasing attention to salt-tolerant rice development. However, it takes a long time, has a relatively low success percentage, and has primitive parental selection progress, so conventional breeding methods must be improved. Combining molecular approaches and conventional breeding methods can be a promising approach to developing salt-tolerant rice to ensure food security. In this chapter, we will explain how conventional breeding methods can be combined with modern molecular methods and new approaches can be developed.

Understanding the rules that govern microbial community assembly is essential for predicting ecosystem function. While microbial predators are key biotic agents that shape bacterial communities through predation, yet their ecological consequences have been studied mostly in isolated and in vitro systems[1][1]–[3][2]. In contrast, large-scale studies of microbial diversity have primarily emphasized abiotic factors as drivers of community assembly [4][3]–[7][4], while the role of microbial predators modulating global microbial divergence and convergence patterns remains largely neglected. Here, we show that bacterivorous protists (predators) exert dual, scale-dependent effects on microbial communities: promoting local convergence by suppressing dominant bacterial taxa, while generating global divergence through species-specific predation effects. By integrating global meta-analyses, controlled field experiments, and reconstructions of natural and synthetic communities, we find that predator identity and prey susceptibility jointly determine convergence outcomes. Communities dominated by predator-resistant taxa exhibit reduced convergence under predation pressure, revealing a predictable trait-based filtering mechanism. This framework reconciles previous contradictory findings[3][2],[8][5]–[11][6] and highlights predators as selective, context-dependent agents of microbial biogeography. Predator-driven convergence suggests new opportunities for microbiome engineering [12][7]: targeted use of predators may steer microbial communities toward functional configurations that enhance soil health, disease suppression, carbon cycling, and ecosystem resilience [2][8],[13][9],[14][10]. ### Competing Interest Statement The authors have declared no competing interest. Japan Society for the Promotion of Science (JSPS), JP22K14804, JP25K02147, JP24K01654 [1]: #ref-1 [2]: #ref-3 [3]: #ref-4 [4]: #ref-7 [5]: #ref-8 [6]: #ref-11 [7]: #ref-12 [8]: #ref-2 [9]: #ref-13 [10]: #ref-14

The plant-microbe interactions, which is crucial for plant health and productivity, mainly occur in rhizosphere: a narrow zone of soil surrounding roots of living plants. The rhizosphere hosts one of the most intense habitats for microbial prey-predator interactions, especially between predatory protists and bacteria. Here, based on two key facts, microbial predators modulate rhizobacterial community composition, and the rhizobacterial community is the primary source of root microbiome, endophytes; we hypothesized that predation upon rhizobacteria would modulate the community composition of endophytic bacteria. The effects of three taxonomically distinct axenic protist species (Acanthamoeba castellanii, Vermamoeba vermiformis, and Heteromita globosa) were tested in this study. To examine the robustness of the hypotheses, the experiments were conducted in three soil types characterized by distinct bacterial communities and physicochemical properties. The bacterial community compositions were analyzed with high throughput sequencing. Bacterial gene abundances were estimated with a real-time-PCR method. The results showed that protists modulated endophytic communities, which originated in the rhizosphere soil. The modulation of endophytic communities by protists showed chaotic patterns rather than a deterministic effect under different soil types. The observed chaotic dynamics were further confirmed with an additional experiment, in which chaos was triggered by changes in the dilution rates of soil nutrients. Furthermore, the presence of predators enhanced the root colonization of endophytes. Our findings identify a key mechanism for the modulation of root endophytes and enhance understanding of underground plant-microbe interactions, which can lead to open new avenues for modulating the root microbiome to enhance crop production.

Transgenerational plasticity in plants enables rapid adaptation to environmental changes, allowing organisms and their offspring to adapt to the environment without altering their underlying DNA. In this study, we investigated the transgenerational plasticity in salinity tolerance of rice plants using a reciprocal transplant experimental strategy. Our aim was to assess whether non-genetic environment-induced phenotypic modifications and transgenerational salinity affect the salinity tolerance of progeny while excluding nuclear genomic factors for two generations. Using salt-tolerant and salt-sensitive rice genotypes, we observed that the parentally salt-stressed salt-sensitive genotype displayed greater growth performance, photosynthetic activity, yield performance, and transcriptional responses than the parentally non-stressed salt-sensitive plants under salt stress conditions. Surprisingly, salt stress-exposed salt-tolerant progeny did not exhibit as much salinity tolerance as salt stress-exposed salt-sensitive progeny under salt stress. Our findings indicate that the phenotypes of offspring plants differed based on the environment experienced by their ancestors, resulting in heritable transgenerational phenotypic modifications in salt-sensitive genotypes via maternal effects. These results elucidated the mechanisms underlying transgenerational plasticity in salinity tolerance, providing valuable insights into how plants respond to changing environmental conditions. Parental environmental experiences induce heritable epigenetic changes in offspring: maternal effects lead to the production of salt-tolerant progeny from salt stress-sensitive rice genotypes, revealing transgenerational phenotypic modifications.

The increasing global population and climate change threaten food security, with the need for sustenance expected to rise by 85% by 2050. Rice, a crucial staple food for over 50% of the global population, is a major source of calories in underdeveloped and developing countries. However, by the end of the century, over 30% of rice fields will become saline due to soil salinity caused by earthquakes, tsunamis, and rising sea levels. Plants have developed strategies to deal with salt stress, such as ion homeostasis, antioxidant defense mechanisms, and morphological adaptations. Proline, an endogenous osmolyte, is the predominant endogenous osmolyte that accumulates in response to salinity, and its overexpression in rice plants has been observed to increase plant salinity tolerance. Exogenously applied proline has been shown to improve plant salt tolerance by reducing the destructive effect of salinity. Recent research has focused on ionic toxicity, nitrogen fixation, and gene expression related to salt tolerance. Exogenous proline has been shown to improve water potential and leaf content, restoring water usage efficiency. It can also ease growth inhibition in salt-sensitive plants. Exogenously applied proline increases antioxidant activities and enhances plant salinity tolerance. This review examines the role and processes of proline in rice plants under salt stress and its relationship with other tolerance mechanisms.

Rice is one of the most important staple foods globally, sustaining over half of the world’s population. However, the sustainability of grain production is increasingly threatened by heat stress, which is intensified by global climate change. Heat stress, characterized by temperatures exceeding crop-specific optimal growth thresholds, significantly impacts the rice yield and quality, particularly during critical reproductive stages. This review synthesizes current research on strategies to mitigate heat stress in rice through genetic and agronomic approaches. It highlights the implementation of advanced genetic tools such as marker-assisted selection (MAS) and genomic selection (GS) to accelerate the breeding of heat-tolerant rice varieties. Additionally, it discusses sustainable agronomic practices, including adjusting planting dates, optimizing water management, and crop rotation, which enhance resilience to heat stress. The objective of this review is to bridge the gap between research findings and practical agricultural applications, providing a comprehensive resource that guides future research directions and informs policy interventions. This review emphasizes the importance of integrating genetic innovations with traditional and modern farming practices to develop rice varieties that can withstand the adverse effects of heat stress, ensuring food security and agricultural sustainability in the face of climatic challenges.

High temperatures, drought, and salt stresses severely inhibit plant growth and production due to the effects of climate change. The Arabidopsis ARR1, ARR10, and ARR12 genes were identified as negative salt and drought stress regulators. However, in rice, the tolerance capacity of the hst1 gene, which is orthologous to the ARR1, ARR10, and ARR12 genes, to drought and multiple high temperature and drought stresses remains unknown. At the seedling and reproductive stages, we investigated the drought (DS) high temperature (HT) and multiple high temperature and drought stress (HT+DS) tolerance capacity of the YNU31−2−4 (YNU) genotype, which carries the hst1 gene, and its nearest genomic relative Sister Line (SL), which has a 99% identical genome without the hst1 gene. At the seedling stage, YNU demonstrated greater growth, photosynthesis, antioxidant enzyme activity, and decreased ROS accumulation under multiple HT+DS conditions. The YNU genotype also demonstrated improved yield potential and grain quality due to higher antioxidant enzyme activity and lower ROS generation throughout the reproductive stage under multiple HT+DS settings. Furthermore, for the first time, we discovered that the B−type response regulator hst1 gene controls ROS generation and antioxidant enzyme activities by regulating upstream and downstream genes to overcome yield reduction under multiple high temperatures and drought stress. This insight will help us to better understand the mechanisms of high temperature and drought stress tolerance in rice, as well as the evolution of tolerant crops that can survive increased salinity to provide food security during climate change.

Salinity poses a significant challenge to global wheat production. The screening of wheat cultivars for salt tolerance is essential for developing new varieties resilient to salinity and advancing breeding strategies. Identifying key traits from a myriad of morphological, physiological, and molecular markers in screening studies can enhance selection efficiency and expedite the process. In this study, 16 common wheat cultivars were subjected to 0 and 150 mM NaCl stress for ten days during the seedling stage. To assess the salinity tolerance of wheat cultivars comprehensively, we employed a diverse array of morpho-physiological, biochemical, and molecular markers, coupled with multivariate analysis. Salt stress resulted in reduced germination and seedling growth across most wheat cultivars. Notably, the ‘Ikizce-96’ and ‘Demir-2000’ genotypes exhibited a higher salinity tolerance index, with the least reduction in morpho-physiological parameters. These cultivars demonstrated elevated osmoregulator proline content and enhanced activity of reactive oxygen species-scavenging antioxidant enzymes. Under 150 mM NaCl, tolerant cultivars exhibited up-regulated transcript expression levels of TaHKT1;4, TaP5CS, and TaDHN marker genes compared to salt-sensitive cultivars. The accuracy of our findings was validated through principal component analysis, hierarchical clustering analysis, and a correlation network. Proline content, glutathione reductase, catalase, and superoxide dismutase activity emerged as the most reliable indicators of salt tolerance in wheat under saline conditions. The identified salt-tolerant cultivars hold promise as donor parents in salinity tolerance breeding programs.

Biofertilizers offer a sustainable method for improving rice growth and productivity, yet their effects on the interaction between plant growth, photosynthetic activity, and gene expression remain under-researched. This study examines how biofertilizer influences rice physiology, focusing on photosynthetic regulation and expression of chlorophyll-related genes. Eight fertilizer treatments were applied: control (CNT), biofertilizer (BF), deactivated biofertilizer (DABF), rice straw (RS), rice straw with biofertilizer (RS+BF), organic fertilizer (OF), organic fertilizer with biofertilizer (OF+BF), and inorganic fertilizer (IOF). Plant height, tiller number, SPAD, NDVI, chlorophyll content, and photosynthesis rates were measured, while gene expression analysis was conducted using RT-qPCR. The OF+BF treatment produced the most significant results, leading to a 31% increase in plant height, a 135% increase in tiller number, and a 42% increase in chlorophyll content (SPAD values) compared to the control. Additionally, OF+BF enhanced photosynthetic efficiency by 74%, with the highest net photosynthetic rate of 48.23 μmol CO2 m−2 s−1. Gene expression analysis revealed that OF+BF upregulated key photosynthesis-related genes, such as OsChlD and OsCHLM, showing a 70% and 90% increase in expression. These findings highlight the potential of integrating biofertilizers with organic fertilizers to sustainably boost rice growth and productivity, contributing to global food security and climate change mitigation.