The aim of this research is to understand how cover crop species combined with different times of N application affect the cover crop straw, nutrition and productivity of cash crop, soil chemical properties and soil microbial composition and function in a holistic approach of the entire agricultural system under tropical no-till system. Focus is on microbiome that immediately respond to the N application disturbances and in a long period to the plant cultivation, N inputs and soil properties changes. We use 3-year field experiment with palisade grass and ruzigrass cover crops and subsequent maize cash crop combined with different N management strategies to quantify the microbial genes of the N cycle and the bacterial and fungal communities’ structure and composition in the agricultural system.

Unsustainable agricultural management practices such as non-conservationist tillage and overuse of fertilizers result in soil acidity and, in turn, soil degradation due to reduced carbon (C) concentrations and nutrient availability and increased aluminum toxicity. Application of lime (L) and phosphogypsum (PG) can overcome these constraints and improve soil quality, but the long-term effects of these amendments on both abiotic and biotic soil properties are not known, particularly when applied in combination. Here, we evaluate the effects of L (acidity corrective), PG (soil conditioner), and their combination (LPG) on soil organic matter (SOM) transformations, soil chemical and physical properties, microbiome assembly, N uptake by intercropped plants, maize yield, archaeal and bacterial abundances, and N cycle genes in the maize and ruzigrass rhizospheres in a long-term field experiment in tropical soil with a no-till maize and forage ruzigrass intercropping system. 

Land degradation usually leads to a reduction in soil fertility, decline of plant productivity, and loss of biodiversity. Introducing beneficial microbial inoculants to degraded lands represents a promising and sustainable strategy. The aim of this project is to reveal the ecological roles of microbial inoculants and soil-resident microbial community in restoring both belowground biodiversity and aboveground productivity in the degraded land.

The global saline-alkali land area has already exceeded 1.1 billion hectares. China has about 100 million hectares. Rice cultivation has been used as an effective strategy to amend saline-alkaline lands in northeastern Songnen Plain in China since the 1950s. However, it is not known the role of microbial functions during succession of soil restoration. The aim of this project is to fundamental understanding the microbial functions succession during the saline soil restoration.

In Bio-Based Economy, plant materials are an essential resource for new industrial and sustainable applications. To ensure the production of sufficient plant biomass there is a need of mineral fertilizers. However, intensive fertilization causes leaching and run-off of nutrients, reduction in biodiversity, production of greenhouse gasses, global warming and changes in soil pH leading to environmental degradation. A key challenge is to intensify agricultural production methods in a way that minimizes harmful environmental effects of fertilizers. Therefore, there is an urgent need for new strategies that optimize plant growth and minimize abiotic and biotic factors that adversely affect plant growth and quality. The plant microbiome, i.e. the collective microbial communities associated with plants, harbors various fungal and bacterial genera that have beneficial effects on plant growth and health. Several bacterial genera promote plant growth and induce systemic resistance in plants against pathogens as well as insect pests. Recent 'omics'-based studies revealed that specific rhizobacteria cause substantial transcriptional changes in plants, leading to elevated levels of specific plant genes expression. Brazilian sugarcane production system is being developed towards to sustainable manner by recycling straw and vinasse (byproduct of ethanol industry), which combined practices allow less mineral fertilizers to be added into soil. In addition, the use of beneficial bacteria, such as plant growth promoting bacteria (PGPB) isolated from sugarcane rhizosphere has shown to increase plant growth and health under controlled situation. However, detailed investigation and fundamental understanding of the effect of these PGPB in different sugarcane genotypes in different soils containing different microbial community are urgent need. Therefore, this proposal aims to: (i) determine the effect of different soil microbial community composition on sugarcane growth inoculated with PGPB; (ii) identify the PGPB traits and genes involved in plant growth promotion; (iii) identify the plant traits and genes involved in plant growth promotion induced by PGPB. Potential applications of this proposal will be (i) the identified PGPB traits and genes to ensure or enhance plant biomass, yield and quality; (ii) the identified genotype-specific genes induced by PGPB responsible for enhancing plant productivity. The proposed project will provide new insights into mechanisms, traits and genes underlying PGPB-plant interactions and will yield new leads and tools to ensure/enhance sugarcane biomass for bio-based economy

Plant-growth promoting microbes (PGPM) are a viable alternative to traditional fertilizers for enhancing plant productivity and improving soil quality without environmental pollution. The use of PGPM in agriculture has been hampered by a lack of reproducible results and the difficulty of transferring this technology to the field. This inconsistent success primarily reflects competition or resistance of the original soil microbiome to inoculants, as well as the negative effects of management practices such as fertilization on plant interactions with the soil microbiome and the efficiency of ecosystem services delivered by PGPM. We were the first to circumvent this problem under field conditions by manipulating the soil microbiome to successfully obtain consistent, positive effects of inoculated microbes on plant productivity (Cipriano et al., 2016;https://doi.org/10.1093/femsec/fiw197). However, the influence of the indigenous soil microbiome on plants remains largely unknown. We propose to investigate this tripartite, PGPM-plant-soil microbiome interaction in plant quality and productivity using state-of-the-art ‘omics’ and bioinformatics approaches to investigate facilitation (positive interactions) and competition (negative interactions) by both microbes and PGPM within the plant realized niche following gradients of both soil diversity and nutrient availability. This research will facilitate the development of innovative methods for agricultural and horticultural starting material production using PGPM for sustainable crop production by combining techniques to reduce nutrient input and enhance the efficiency and long-lasting effects of PGPM. This research proposal will integrate approaches to obtain a fundamental understanding of these tripartite interactions in a smart microbiome engineered plant production system for sustainable high-quality crop production.

Microp- Stress-induced communication between plants and microbes

MiRA- Microbe-induced Resistance to Agricultural pests

VolControl will examine the possibility to enhance control of soil-borne fungal crop diseases via stimulation of production of pathogen-suppressing volatiles by soil microbes. The working hypothesis is that these volatiles will be released by bacteria upon decomposition of selected organic materials that contain precursors of suppressive volatiles. During the first phase of the project, different organic materials will be screened and the ones that give the most promising results will be further tested for disease suppressing performance in greenhouse - and field trials. In addition, information will be provided on the identity of the produced suppressing volatiles and the microbes that release these volatiles. The project will be done in close collaboration with participating companies to optimize application perspectives

This is a sub-project of a WUR-NIOO project entitled "Closing the loop: exploiting sustainable insect production to improve soil, crop and animal health", coordinated by Prof. Marcel Dicke. Insects can transform waste streams into high-value proteins for food and feed. Consequently, insects provide valuable contributions to a circular economy. The project aims to investigate the valorisation of the rest-stream of insect production, i.e. moulting skins and faeces (‘frass’) to enhance soil health and crop health (https://doi.org/10.1016/j.tplants.2022.01.007).
In the NIOO project, we study the decomposition rate of frass and moulting skins of three insects species (black soldier fly, mealworm, cricket) in arable soil as well as the composition of the fungal and bacterial decomposers. In addition, we study if the insect materials, which are rich in chitin, can be used to control soil-borne fungal plant diseases.