Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities

Guo, Sai; Xiong, Wu; Xu, Hang; Hang, Xinnan; Liu, Hongjun; Xun, Weibing; Li, Rong

doi:10.1016/j.ejsobi.2018.05.007

Cited by 29 publications

(18 citation statements)

References 33 publications

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“…While linking agricultural management to large-scale outcomes such as nutrient fluxes or ecosystem services requires an analysis of bulk soil properties and processes, understanding the complex relationship between management practices and plant nutrition and productivity necessitates shifting the focus to the rhizosphere (20). Some evidence suggests that management can affect the ecosystem-level functions carried out by bulk soil microbial communities through impacts on microbial diversity (21), but the unique chemistry and microbial communities found in the rhizosphere (22) are more closely linked to plant outcomes of agricultural importance (23). Because rhizosphere soil is shaped by complex interactions between plant and bulk soil processes, the effects of agricultural management on rhizosphere communities and the functional implications are not always easy to predict.…”

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confidence: 99%

“…The few studies that have addressed this question have concluded that differences in bulk soil microbial and protist communities do carry over to some extent to rhizosphere communities (22,24). However, such studies have frequently been conducted on long-term research stations (22,24), leaving open the questions of scale and context. Do management effects on rhizosphere microbial communities extend to an intermediate scale, such as paired fields within a region?…”

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confidence: 99%

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Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

Schmidt

Vannette

Igwe

et al. 2019

Appl Environ Microbiol

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Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO 3 -N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity. IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.

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mentioning

confidence: 99%

mentioning

confidence: 99%

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

Schmidt

Vannette

Igwe

et al. 2019

Appl Environ Microbiol

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“…However, the taxonomic resolution of these morphogroup-approaches is low, with individual morphogroups consisting of phylogenetically and functionally diverse taxa [19] and might therefore undermine important ecological differences. High-throughput sequencing approaches now enable a deeper resolution of protist communities and have revealed that long-term mineral fertilization reduced protist diversity in soils compared with organic fertilization [22]. In contrast, Lentendu et al [23] reported that organic fertilizers more strongly altered protist communities than mineral fertilizers.…”

Section: Introductionmentioning

confidence: 99%

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils

et al. 2019

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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. Electronic supplementary material The online version of this article (10.1186/s40168-019-0647-0) contains supplementary material, which is available to authorized users.

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“…This is, for example, the case of Sphagnum and peatland-mosses-associated protists for which both V4 (TAReuk) and V9 (1380F/1510R) primers have been used [ 137 , 138 ]. Both V4 (V4_1f/TAReukREV3) and V9 (1380F/1510R) primers have also been employed to study rhizospheric protists [ 139 , 140 ]. Although plant sequences could represent the majority of reads in such plant-associated protist metabarcoding datasets, strategies to reduce the co-amplification of the associated plant(s), for example, the utilization of blocking oligos, have not yet been implemented.…”

Section: Amplicon Library Preparationmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

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Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities

Cited by 29 publications

References 33 publications

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

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