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Irrigated and rain-fed rice fields are unique agroecosystems and anthropogenic wetlands whose main feature is seasonal flooding. Flooded soils are characterized by spatiotemporal shifts and oscillation of the oxygen status and redox potential, sustaining varieties of microbial metabolisms, where bacteria and methanogenic archaea play principal roles and thus have been the major research targets. In this review, we focus on the diversity and ecology of protists—often overlooked biological entities—in wetland rice field soils. Protists with different ecological functions, i.e., phagotrophs, phototrophs, saprotrophs, and parasites, inhabit a rice field soil with a community- and individual-level adaptation to the wide range of oxygen tensions and redox potential. Other agricultural managements like fertilization and char application also influence the protist community. They link to the material cycling in rice soil and affect the activities and community composition of the microorganisms involved in the biogeochemical cycles. Rice roots are the hot spot for protists, which control the rhizospheric bacterial community and could increase the plant productivity through enhancing nutrient release and altering bacterial activities. This review highlights the essential roles of protists in a wetland rice field soil and needs for further research to fill the gaps in knowledge regarding the diversity and functions of the protists in this unique agroecosystem.

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. Microbial communities shape ecosystem functioning, yet why they differ across spatial scales remains unclear. This study shows that bacterivorous protists shape microbial diversity by promoting local convergence while generating global divergence.

Biological methane oxidation is a key process in the methane cycle of wetland ecosystems. The methanotrophic biomass may be grazed by protozoa, thus linking the methane cycle to the soil microbial food web. In the present study, the edibility of different methanotrophs for soil protozoa was compared. The number of methanotroph-feeding protozoa in a rice field soil was estimated by determining the most-probable number (MPN) using methanotrophs as food bacteria; naked amoebae and flagellates were the dominant protozoa. Among ten methanotrophic strains examined as a food source, seven yielded a number of protozoa comparable with the yield with Escherichia coli [10⁴ MPN (g soil dry weight)⁻¹], and three out of four Methylocystis spp. yielded significantly fewer numbers [10²-10³ MPN (g soil dry weight)⁻¹]. The lower edibility of the Methylocystis spp. was not explained either by their growth phase or by harmful effects on protozoa. Incubation of the soil under methane resulted in a higher number of protozoa actively grazing on methanotrophs, especially on the less-edible group. Protozoa isolated from the soil demonstrated a grazing preference on the different methanotrophs consistent with the results of MPN counts. The results indicate that selective grazing by protozoa may be a biological factor affecting the methanotrophic community in a wetland soil.

Biochar-induced changes in microbial communities are exclusively derived from the studies on the soil bacterial and fungal communities, and we lack an understanding of how biochar can affect taxonomic and functional communities of protists. Here, the short-term effects of two biochars originating from rice husk and poultry litter (hereinafter referred to as RH and PL, respectively) on taxonomic and functional community compositions of protists in a rice rhizosphere were studied using high-throughput sequencing. Soil physicochemical properties were differentially affected by the RH and PL amendments. The relative abundance of Stramenopiles, mainly oomycetes (Peronosporomycetes), was increased in the RH-amended soil, which was correlated with the increased total pore volume and C/N ratio. In the PL amended soil, the relative abundances of Amoebozoa, Alveolata, and Excavata were increased, and those increases were correlated with the enhanced pH and nutrient conditions. Among functional groups, the relative abundance of phagotrophic protists increased by the PL amendment, while the relative abundance of plant pathogens was decreased by both the RH and PL amendments. Network analysis indicated that phagotrophs were the keystone group and were sensitive to the biochar amendments. The keystone taxa in each biochar treatment were different: Cercozoa (Rhizaria) in control, Conosa (Amoebozoa) in RH, and Discoba (Excavata) in PL. The impact of biochar on protist communities correlated with its physicochemical properties, which depends on the source material.

PurposeTo reveal whether microaerophilic Fe(II)-oxidizing bacteria (FeOB) participate in the Fe(II) oxidation at the oxic-anoxic interface in flooded paddy field soil, distribution of microaerophilic FeOB belonging to Gallionellaceae (Gallionella-related FeOB) in the surface layer of a flooded paddy soil microcosm and O2 conditions for the Fe(II) oxidation by a microaerophilic Fe(II) oxidizer, Ferrigenium kumadai An22, were investigated.Materials and methodsFlooded paddy soil microcosms were incubated for 30 days. Five soil layers were sampled at 2-mm intervals from the soil surface after the incubation. The community structure of Gallionella-related FeOB was analyzed with qPCR and DGGE methods. In the culture experiment, O2 and Fe(II) profiles in F. kumadai An22-inoculated and non-inoculated gel-stabilized gradient tubes were analyzed, in which an opposing gradient of O2 and Fe(II) was formed.ResultsA thin oxic layer was formed at the soil surface after the incubation. The copy number of 16S rRNA genes of Gallionella-related FeOB was highest at the top 0–2 mm layer of the soil. DGGE analysis showed that several bands derived from Gallionella-related FeOB newly appeared at the top soil layer with high intensity. In the culture experiment, F. kumadai A22 grew at the oxic side of the oxic-anoxic interface with the formation of Fe oxides.ConclusionThe present study indicated that Gallionella-related microaerophilic FeOB proliferated in the surface layer of flooded paddy field soil, presumably by oxidizing Fe(II) in the oxic-anoxic interface.

The effects of protists on an indigenous soil bacterial community, putative bacterial genes involved in N-cycling, and the rice plant growth were studied in poultry litter biochar (PL) and rice husk biochar (RH) amended (with two application doses: 2% and 4% w/w) paddy field soil. The bacterial community composition, which was evaluated using 16S rRNA gene amplicon sequencing, was significantly and differentially affected by the protists, the PL and the RH. The effects of protists on the bacterial community composition were decreased by the RH and the PL treatments. The number of protist-affected bioindicator bacterial taxa was decreased from 90 to 46, 29, 43, and 21 in the 2% RH-, 4% RH-, 2% PL-, and 4% PL-treated soils, respectively. The presence of the protist significantly increased the abundance of the putative bacterial genes involved in mineralisation, dissimilatory nitrate reduction to ammonium (DNRA), and NO3- assimilation, and the same occurred with PL treatments. The rice plant growth and N uptake were always higher in the presence of protists and PL amendments. Overall our results suggest a new insight into the effects of biochar on the bacterial community via altering the trophic interactions.

Rice grain yield prediction with UAV-driven multispectral images are re-emerging interests in precision agriculture, and an optimal sensing time is an important factor. The aims of this study were to (1) predict rice grain yield by using the estimated aboveground biomass (AGB) and leaf area index (LAI) from vegetation indices (VIs) and (2) determine the optimal sensing time in estimating AGB and LAI using VIs for grain yield prediction. An experimental trial was conducted in 2020 and 2021, involving two fertility conditions and five japonica rice cultivars (Aichinokaori, Asahi, Hatsushimo, Nakate Shinsenbon, and Nikomaru). Multi-temporal VIs were used to estimate AGB and LAI throughout the growth period with the extreme gradient boosting model and Gompertz model. The optimum time windows for predicting yield for each cultivar were determined using a single-day linear regression model. The results show that AGB and LAI could be estimated from VIs (R2: 0.56–0.83 and 0.57–0.73), and the optimum time window for UAV flights differed between cultivars, ranging from 4 to 31 days between the tillering stage and the initial heading stage. These findings help researchers to save resources and time for numerous UAV flights to predict rice grain yield.

Zinc (Zn) is often of deficient in paddy soils, and optimizing its application is crucial for improving maize productivity in intensive rice–maize cropping systems. This study aimed to develop practical Zn fertilizer strategies suitable for paddy soils with varying pH levels, thereby improving nutrient management and understanding of soil microbial responses. Field experiments were conducted during the 2020–2021 dry seasons at three sites: Chon Daen (pH 5.8), Noen Maprang (pH 6.7), and Lom Sak (pH 7.8). A two-factorial randomized complete block design with four replications was used, including four ZnSO4·H2O rates (0, 1.5, 3, and 6 times the DTPA-extractable Zn in soil) and two hybrid maize varieties, Suwan 5731 and Suwan 5819. Results showed that at Chon Daen, Zn application significantly enhanced shoot Zn uptake and soil Zn concentration, with SW5819 exhibiting greater Zn efficiency and biomass production. At Noen Maprang, Zn application did not significantly affect dry matter, while, at Lom Sak, Zn responses were moderate, though SW5819 maintained better growth and Zn uptake. Across sites, maize Zn efficiency was highest under acidic conditions and in SW5819. Soil microbial communities remained largely unaffected by Zn fertilization and were primarily influenced by soil pH, with Proteobacteria, Crenarchaeota, and Ascomycota dominating bacterial, archaeal, and fungal groups, respectively. These findings support the feasibility of Zn fertilization strategies to enhance both crop productivity and nutritional quality without altering the microbial community composition.

Zinc (Zn) fertilization is widely used in maize (Zea mays L.) production to alleviate Zn deficiency and improve biomass and grain yield. However, limited research exists on Zn management in maize cultivated in high-pH paddy soils following rice-based systems, where altered soil chemistry may affect Zn availability and plant uptake. This study aimed to evaluate the effects of Zn application rates on growth, yield, and Zn uptake in two hybrid maize varieties under such conditions. Field experiments were conducted during the 2019 and 2020 dry seasons in Phetchabun Province, Thailand, using a randomized complete block design with a 4 × 2 factorial arrangement and four replications. Treatments included four Zn rates (0, 5, 10, and 20.6 kg of Zn/ha), applied as Zn sulfate monohydrate (ZnSO4·H2O, 36% Zn) by soil banding at the V6 stage, and two hybrid varieties, Suwan 5731 (SW5731) and Suwan 5819 (SW5819). In 2019, significant Zn × variety interactions were observed for biomass, crop growth rate (CGR), and grain yield. SW5819 at 10 kg of Zn/ha produced the highest biomass (31.6 t/ha) and CGR (25.6 g/m2/day), increasing by 15.3% and 39.1%, respectively, compared to its own no Zn treatment. In contrast, 20.6 kg of Zn/ha reduced SW5819 biomass by 6.6% and 13.1% relative to SW5731 and its own no-Zn treatment, respectively. Grain yield in SW5819 peaked at 14.7 t/ha under 5 and 10 kg of Zn/ha, significantly higher than SW5731 under 0 and 5 kg of Zn/ha by 16.7%, while SW5731 showed no significant response. In SW5819, shoot and grain Zn uptake significantly increased under 5 and 10 kg of Zn/ha by up to 36.8% and 33.3%, respectively, compared to no Zn treatment. The lowest shoot Zn uptake was found in SW5819 under 20.6 kg of Zn/ha (264.1 ± 43.9 g/ha), which was lower than all its Zn treatments and all SW5731 treatments, showing a reduction of 19.4–43.6%. Zn application improved soil Zn availability, and Zn partitioning among plant organs varied with Zn rate and season. A moderate Zn rate (10 kg of Zn/ha) optimized maize performance under high-pH, rice-based conditions, emphasizing the need for variety-specific Zn management.