Márcio Leite

Dr. ir. Márcio Leite PhD

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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands



At NIOO, I want to get the help of soil microbes to make agriculture more sustainable.


2017 - 2022

PhD in Environmental Biology, Utrecht University, Utrecht, Netherlands.

2014 - 2022

PhD in Agroecology, Maranhão State University, São Luís, Maranhão, Brazil.

2012 - 2014

Msc. in Agroecology, Maranhão State University, São Luís, Maranhão, Brazil.

2007 - 2011

Bsc in Environmental Engineering, CEUMA University, São Luís, Maranhão, Brazil

Research groups



  • 2019–2022
    Junior Researcher
  • 2022–Present


  • 2007–2011
    Environmental Engineering (CEUMA University)
  • 2012–2014
    Msc. Agroecology (State University of Maranhão)
  • 2017–2022
    PhD Ecology and Biodiversity (Utrecht University)

PhD students

  • 2019–Present
    Cristina Rotoni
    Netherlands Institute of Ecology
    Promotors and Copromotors: Prof. Dr. Eiko Kuramae
  • 2022–Present
    Lena Faller
    Netherlands Institute of Ecology
    Promotors and Copromotors: Prof. Dr. Eiko Kuramae

Projects & collaborations


  • Microbial Farming to increase plant productivity

    Project 2018–Present
    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.
    Soil microbial farming to increase plant productivity: reducing nutrient inputs to increase plant-microbe interactions and managing soil microbial diversity
  • Phosphorus use efficiency in Eucalyptus and the microbiome involved

    Project 2018–Present
    Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this project we examine the rhizosphere bacterial and fungal including Arbuscular Mycorhizal Fungi (AMF) communities of young plants of 24 species of eucalypts (22 Eucalyptus and two Corymbia species) under low or sufficient soil P availability.
  • Harnessing the rhizosphere microbiome to enhance plant productivity

    Project 2015–Present
    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
  • REPHORM - REcycled PHOsphorus Resolved by Microbes

    Project 2022–Present
    Sufficient Phosphorus (P) and Iron (Fe) supply is essential for crop production. Most of the P and Fe in soil is not readily available for the plant, making agriculture depending on inorganic fertilizers mainly derived from depletable resources. An alternative to this unsustainable practice is to use recycled compounds recovered during wastewater treatment. This project focuses on the use of the two recycled compounds struvite (MgNH4PO4·6H2O) and vivianite (Fe3(PO4)2·8H2O) which are both insoluble and hard to synchronize with the nutrient needs during early plant development. To increase efficient nutrient release of these recycled sources, we propose the use of microbes that can solubilize P and release siderophore, both recognized traits of plant growth promoting microbes. Several plant growth-promoting microbes have been isolated, but their transfer to agriculture, so far, resulted in an inconsistent success, due to competition or resistance of the resident soil microbiome to inoculants. This project will circumvent this challenge by steering the local microbiome with the addition of recycled nutrients and will further optimize the microbiome by microbial community breeding. Overall, this project will focus on identifying microbial community members with struvite and vivianite solubilizing function, optimizing these communities, determining the role of these communities on increasing the nutrient release as well as monitoring the recruitment of these beneficial microbes in the rhizosphere and the effect on plant growth.
  • Restoring degraded lands with microbial inoculants

    Project 2019–Present
    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.
    Degraded land