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Background Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. Results We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. Conclusions Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.

Background Biological control (biocontrol) organisms are the key component of the sustainable agriculture. Although the majority of the research on biocontrol organisms focused on fungi and bacteria, recent studies revealed the importance of predatory protists in pathogen suppression through direct (by feeding on plant pathogens) and indirect (by enhancing bacterial activities related to pathogen suppression) mechanisms. However, a review of the literature related to predatory protists and plant pathogen interaction is still lacking. Scope In this review, we aimed to 1) provide the current body of knowledge on the roles of predatory protists in plant pathogen suppression, and 2) highlight the importance of predatory protists as potential biocontrol agents. We also provided information on isolation techniques and application methods of predatory protists that can be used as biocontrol agents in agricultural systems. Conclusion We highlighted that predatory protists can be an important solution for the sustainable management of plant pathogens. Since there is a huge knowledge gap in this area, further studies should focus on protist-pathogen interaction and its application for sustainable plant productivity.

Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.

Aims The general aim of the study is to provide insight into the importance of functioning maintenance of forest ecosystems. Specifically, the aim of the study is to assess the response of soil protist diversity, composition and co-occurrence network to varying degree of decomposition of fallen wood when compared to conventional soil. Methods A total of 24 samples of soil and fallen wood were collected from subtropical broad-leaved forests in China. Here we use a correlative approach to link the community of soil protists with fallen wood at different decomposition stage and compare with fallen-wood-free soil. The indicators of protists community were assessed using DNA metabarcoding of the 18S rRNA (Illumina sequencing). Results The biodiversity of soil protists tended to increase as decomposition advanced and pronounced difference was found between severe and moderate decomposition stages ( P  < 0.05). The decomposition of fallen wood had a significant effect on the composition of the soil protist community (Adonis: R 2  = 0.24, P  < 0.01), and enhanced the complexity and stability of the co-occurrence network of soil protists. Soil protists exhibited a stronger association with fallen wood (11 significant linkages), compared to soil (7 significant linkages). Fallen wood decomposition indirectly affected the soil protist community through multiple ways. Conclusions Retention of fallen wood helps maintain the richness and interaction of soil protists. Future research directions should focus on specific mechanisms for how fallen wood decomposition affects protists. Our work may contribute to better guide forest management policies in China.

Geosmin is a volatile organic compound (VOC) produced by a range of different soil microorganisms, and is most commonly recognized for its characteristic “earthy” scent evident after rainfall. Though it remains unclear why microorganisms produce geosmin, we know that exposure to geosmin can influence behaviors across a wide range of organisms, serving as both an attractant and a repellant, but geosmin effects on soil protists remain largely unstudied. We investigated how soil protists respond to geosmin exposures, focusing on representatives of three morphological groups of protists, Colpoda sp. (ciliate), Cercomonas sp. (flagellate), and Acanthamoeba castellanii (naked amoeba), testing the hypothesis that geosmin production by bacteria influences soil protist behavior. We conducted experiments to evaluate protist excystment (waking up) and predation responses to geosmin-producing ( Streptomyces coelicolor M145) and non-producing ( S. coelicolor J3003) bacteria, as well as synthetic geosmin. All three protists excysted at higher rates when exposed to geosmin-producing bacteria or synthetic geosmin, while no significant excystment occurred with the non-producing strains or in the absence of synthetic geosmin. Protist feeding preferences were also affected, with two of the three protists ( Cercomonas sp. and A. castellanii ) less likely to predate geosmin-producing versus non-producing bacterial strains. Our findings suggest that soil protists can detect geosmin as a signal indicating favorable soil conditions and geosmin production by bacteria may serve as a deterrent to predation by protists. More generally, our results highlight the ecological significance of geosmin in the soil food web and its role in mediating bacteria-protist interactions.

Soil protists are rarely included in ecotoxicological investigations, despite their fundamental role in ecological processes. Moreover, testate amoebae and diatoms contribute considerably to silicon fluxes in soils. We investigated the effects of heavy metals on testate amoebae (species and individual densities) and diatoms (individual densities) in aged soils of a floodplain (Watarase retarding basin, Japan) taking soil samples from two unpolluted reference sites and two polluted sites. The total concentrations of Cu, Pb, and Zn in soil were higher at the polluted sites as compared with the reference sites. The available concentrations of Co, Cu, and Zn in CaCl₂ extracts were higher at the polluted sites but available Pb was not detectable. Testate amoeba taxonomic richness was higher in the reference sites (45/38 taxa) than in the polluted sites (36/27 taxa). The reference sites had higher diatom and amoeba densities than the polluted sites. There was a significant negative correlation between total testate amoeba density and heavy metal concentration (available Co), while significant negative correlations were found between diatom density and Co, Cu, and Zn (available and total concentration). Densities of Cyclopyxis kahli cyclostoma, Centropyxis spp., and Trinema complanatum were negatively correlated to concentrations of available heavy metals. The observed decrease in individual numbers due to heavy metal pollution resulted in a considerable decline in protozoic (testate amoebae) and protophytic (pennate diatoms) silicon pools. Our data suggest that heavy metal pollution affects biogeochemical cycling in this system.

Background Reductive soil disinfestation (RSD) is an effective agricultural practice to improve the soil microbial community. However, most RSD research has focused on single bacteria or fungi, little is known about the combined influence on the entire microbiome, particularly impacts on protists and the relationships of these groups linked to plant biomass in rhizosphere soil. Methods In this study, four treatments, i.e., untreated control (CK), RSD with 1% corn straw (CS), 1% miscanthus (MS), and 1% arundo donax (Ad) were performed. Results RSD treatment decreased bacterial and fungal community diversity, but increased the diversity of protistan community, along with the relative abundances of Cercozoa and Amoebozoa belonging to phagotrophic protists. The bacterial community diversity rapidly increased with plant growth in the RSD treatment, and we observed that the bacterial community diversity and structure were the major predictors of plant biomass. The RSD treatment had significantly lower relative abundances of potential pathogenic fungi (e.g., Fusarium and Cladosporium) compared to the CK treatment, and the CK treatment showed a dramatic decrease in fungal community diversity. Additionally, RSD treatment increased both bacteria-bacteria and bacteria-protist connections, as reflected by co-occurrence network analysis. The Mantel test demonstrated that soil pH and NO 3 − -N contents were intensively correlated with bacterial and protistan community diversity, respectively. Moreover, the Ad treatment had notably higher soil LOC and NO 3 − -N contents compared to the CK treatment after 90 days of plant growth. Conclusion RSD treatment promoted plant biomass by increasing soil nutrient turnover and inhibiting pathogen persistence through affecting more connections among soil microbial communities within the rhizosphere.

Oomycetes are a ubiquitous protistan lineage including devastating crop parasites. Although their ecology in agrosystems has been widely studied, little is known of their distribution in natural and semi-natural ecosystems and how they respond to edaphic and environmental factors. We provide here a baseline of the diversity and distribution of soil oomycetes, classified by lifestyles (biotrophy, hemibiotrophy and saprotrophy), at the landscape scale in temperate grassland and forest. From 600 soil samples, we obtained 1148 operational taxonomy units representing ~ 20 million Illumina reads (region V4, 18S rRNA gene). We found a majority of hemibiotrophic plant pathogens, which are parasites spending part of their life cycle as saprotrophs after the death of the host. Overall both grassland and forest constitute an important reservoir of plant pathogens. Distance-based RDA models identified soil type and mineral soil C/N ratio as the most influential factors in shaping oomycete communities in grassland and forest. Edaphic conditions and human-induced management intensification in forest triggered opposite responses in the relative abundances of obligate biotrophs and hemibiotrophs, suggesting different ecological requirements of these two lifestyles.

Purpose Irregular e-waste dismantling has induced serious soil pollution of combined contaminants. The application of lime to paddy soils effectively prevents the accumulation of Cd from soil to rice grains. However, its applicability for rice safety production in the Cd and As contaminated paddy soils has not been well clarified. Methods Lime was applied to three randomized fields across various villages and years to evaluate its applicability. High-throughput sequencing was used to analyze soil bacterial and protist communities. Random forest analysis, variance partitioning analysis, and structural equation modelling were employed to reveal the underlying mechanisms in the regulations on Cd and As accumulation in rice grains. Besides, economic benefit analysis of input and output was performed to compare the applicability of technologies. Results In general, lime incorporation with the XS14 (a rice variety with low accumulation of heavy metals) substantially reduced Cd and As content in the polished rice grains, and met the Chinese food safety standard limits. Statistical analyses illustrated soil abiotic variables mainly drove Cd variances, while soil biotic variables predominantly affected As contents, in the unpolished grains. Particularly, soil protist communities played essential roles in Cd and As content in the unpolished grains, which was affected by soil pH after lime application. Moreover, the output / input ratio was significantly increased by lime addition through rice safety production. Conclusion Lime incorporation with the XS14 overcome the difficulties of the coordinated reductions of Cd and As in rice grains and has strong applicability in combined polluted paddy soils.

Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.