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Galapagos Microbiome Project
An international research team led by the Netherlands Institute of Ecology (NIOO-KNAW) is to search for invisible life in the Galápagos Islands. The diversity of bacteria and other microscopic organisms may not be evident to the naked eye, but it is essential to nature. To the islands' giant daisies, for instance: unique endemic plants that are currently under threat. -
Restoring degraded lands with microbial inoculants
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. -
Long-term Ca-based amendments impact on microbiome and N processes in the rhizosphere and soil in tropical no-till intercropping 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. -
Forage grasses cover crops of rice and maize to steer nitrogen processes and microbiome to mitigate greenhouse gases emissions in long-term tropical agriculture system
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. -
The zooplankton-microbiome (MicroZoo): beyond microbe-host associations
Zooplankton is a crucial component of aquatic food webs -
Back to the Roots - II
The overall goal of the project is to conduct an in-depth analysis of the biodiversity and functions of microorganisms in the spermosphere and (endo)rhizosphere of ancestors of different crops species grown in their native habitat. -
Farming microbial community for plant probiotic - MicroProFarm
A current challenge for modern agriculture is to meet the food production needs for an increasing global population while improving resource use efficiency and attenuating impacts on human health and environment. In order to maximize reliability and stability in agriculture, optimization of crop management and resource use efficiency have been considered the best approaches for a sustainable increase of crop yields under variable agro-ecological conditions, environments and years. For this purpose, one interesting and sustainable method is the use of natural plant biostimulants, a diverse class of products and microorganisms that enhance plant growth and other plant parameters, such as flowering, fruit set, crop productivity and nutrient use efficiency. In this context, several studies already demonstrated that plant biostimulants can induce morpho-anatomical, biochemical, physiological and molecular plant responses, not only improving crop productivity but also promoting protection against abiotic stresses, such as drought and salinity. Among the different biostimulant classes there are protein hydrolysates (PH), mixtures of polypeptides, oligopeptides and aminoacids originated from partially hydrolyzed animal and vegetal tissues. Even though the effect of PH were already observed in diverse crops, the mechanisms and behind their action are still scarcely studied, and their action can vary depending on their origin, characteristics, crop species, cultivars, growing conditions, time and mode of applications, among other parameters. The objective of this project is to evaluate the effect of protein hydrolysates in the growth, nutrient content and microbial communities of crops, if microbes are responsible for these effects, which are the mechanisms and if such effects are long-lasting. -
Matrix - Diversity and functions of the phyllosphere microbiome
In this project we study the taxonomic and functional diversity of the phyllosphere microbiome of wheat. Together with our Danish and US partners, we isolate and characterize yeasts and bacteria living on and in the flag leaf of wheat. The ultimate goal is to identify novel phyllosphere microbes that contribute to tolerance of wheat plants exposed to abiotic and biotic stresses. -
Into Roots - Unwiring regulatory networks in the endophytic microbiome
Plant roots are colonized by billions of microorganisms that affect plant growth and tolerance to (a)biotic stresses. Recently we discovered that plants infected by fungal pathogens actively recruit microbes inside their root tissue, the endosphere, for protection. Here we will investigate how plants under siege communicate with their microbiome and characterize the protective endophytic microbes, their genes and metabolites. With nano-microscopic techniques we will unwire where microbes live inside plant roots and express their protective traits. The obtained fundamental knowledge will provide a strong basis for developing innovative strategies that integrate microbiomes in plant breeding and sustainable crop protection. -
Microbial Farming to increase plant productivity
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.