Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
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ABSTRACT:
PROVIDER: PRJEB25117 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2322300_1.fastq.gz | Fastqsanger.gz | |||
| ERR2322300_2.fastq.gz | Fastqsanger.gz | |||
| ERR2322310_1.fastq.gz | Fastqsanger.gz | |||
| ERR2322310_2.fastq.gz | Fastqsanger.gz | |||
| ERR2322320_1.fastq.gz | Fastqsanger.gz |
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Project description: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.
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Project description:Plant health is the fundamental of agricultural production, which is threatened by plant pathogens severely. The previous studies exhibited the effects of different pathogen control strategies (physical, chemical, and microbial methods), which resulted from bringing in exogenous additives, on microbial community structures and functions. Nevertheless, few studies focused on the potential inhibitory abilities of native microbial community in the soil, which could be activated or enhanced by different fertilization strategies. In this study, three plant diseases (TMV, TBS, and TBW) of tobacco, fungal community of tobacco rhizosphere soil, and the correlation between them were researched. The results showed that nitrogen-reducing fertilization strategies could significantly decrease the occurrence rate and the disease index of three tobacco diseases. The results of bioinformatics analyses revealed that the fungal communities of different treatments could differentiate the nitrogen-reducing fertilization group and the control group (CK). Furthermore, key genera which were responsible for the variation of fungal community were explored by LEfSe analysis. For instance, Tausonia and Trichocladium increased, while Naganishia and Fusicolla decreased under nitrogen-reducing fertilization conditions. Additionally, the correlation between tobacco diseases and key genera was verified using the Mantel test. Moreover, the causal relationship between key genera and tobacco diseases was deeply explored by PLS-PM analysis. These findings provide a theoretical basis for a nitrogen-reducing fertilization strategy against tobacco diseases without exogenous additives and make contributions to revealing the microbial mechanism of native-valued fungal key taxa against tobacco diseases, which could be stimulated by agricultural fertilization management.
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Project description:Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Project description:Soil extracellular enzymes play a significant role in the N mineralization process. However, few studies have documented the linkage between enzyme activity and the microbial community that performs the function. This study examined the effects of inorganic and organic N fertilization on soil microbial communities and their N mineralization functions over 4 years. Soils were collected from silage corn field plots with four contrasting N treatments: control (no additional N), ammonium sulfate (AS; 100 and 200 kg of N ha-1), and compost (200 kg of N ha-1). Illumina amplicon sequencing was used to comprehensively assess the overall bacterial community (16S rRNA genes), bacterial ureolytic community (ureC), and bacterial chitinolytic community (chiA). Selected genes involved in N mineralization were also examined using quantitative real-time PCR and metagenomics. Enzymes (and marker genes) included protease (npr and sub), chitinase (chiA), urease (ureC), and arginase (rocF). Compost significantly increased diversity of overall bacterial communities even after one application, while ammonium fertilizers had no influence on the overall bacterial communities over four seasons. Bacterial ureolytic and chitinolytic communities were significantly changed by N fertilization. Compost treatment strongly elevated soil enzyme activities after 4 years of repeated application. Functional gene abundances were not significantly affected by N treatments, and they were not correlated with corresponding enzyme activities. N mineralization genes were recovered from soil metagenomes based on a gene-targeted assembly. Understanding how the structure and function of soil microbial communities involved with N mineralization change in response to fertilization practices may indicate suitable agricultural management practices that improve ecosystem services while reducing negative environmental consequences.IMPORTANCE Agricultural N management practices influence the enzymatic activities involved in N mineralization. However, specific enzyme activities do not identify the microbial species directly involved in the measured process, leaving the link between the composition of the microbial community and the production of key enzymes poorly understood. In this study, the application of high-throughput sequencing, real-time PCR, and metagenomics shed light on how the abundance and diversity of microorganisms involved in N mineralization respond to N management. We suggest that N fertilization has significantly changed bacterial ureolytic and chitinolytic communities.
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