Vouchering and plant genome sequencing (Wing), Microbiome sampling and analysis (Hirt), Metabolomics sampling and analysis (Al-Babili) and Root development/architecture analysis (Blilou) will establish a robust pipeline and collaborative network to interrogate diverse terrestrial ecosystems, the information of which can used to understand how ecosystems thrive in extreme environments. Such knowledge can be applied to the engineering of large scale ecosystems that promote much needed vegetation cover, to combat desertification, and to promote sustainable agricultural practices throughout the KSA.

Not only will this project produce high-quality ecosystem data sets, it will also train the next generation of ecosystem scientists that will use their skills to create and manage sustainable ecosystems in natural, agricultural and urban settings.

Despite increasing awareness regarding value and importance, the destruction of mangrove forest continues to take place in many parts of the world. At the same time, many countries have recognized the value and importance of mangrove forests and launched restoration projects, which mainly implies replanting of propagules. However, this strategy is only partially successful and many plants do not survive. Among other factors, a key factor is the lack of knowledge on the physical and chemical and biological structure of the respective soils. To counter this deficiency, we therefore propose a soil-tailored engineering approach that is based on the unique availability of a microbial mangrove biobank with the functional analysis of the soil microbiome. In this project, we will assess the feasibility of developing a functional engineering rehabilitation method that replants mangrove propagules with the important microbial partners that are missing in degraded coastal soils.

To succeed in establishing sustainable ecosystems in any soil, requires the consideration of site-specific soil characteristics and microbiomes. Current replanting initiatives will require a knowledge of soil and microbiome status of locations in the coasts. The current project will improve on previous projects by providing synthetic microbial communities that have been tailored to local needs to rehabilitate soils. In short, the AI-based functional analysis of soil sites will determine which microbial pathways and functions are lacking to provide a fertile soil. The lacking pathways will be identified in microbial biobank strains. The advantage of the proposed approach is that the use of synthetic communities based on natural mangrove ecosystems will enhance the success rate in mangrove

Representative view of leaf microbiome of mangrove biobank.

A microbial biobank of 1 000 microbial soil and plant-associated strains was generated. 16S sequencing indicated that the biobank covers all taxonomic and functional groups found in the mangrove ecosystem. As part of this project, the microbial biobank will be sequenced and annotated at the full genome level and used as the resource for assembling the missing microbial units for mangrove  rehabilitation programs  in KSA.

Date palm cultivation is increasingly facing major challenges, including large infestations by red palm weevil (Rhynchophorus ferrugineus) and Bayoud, a fungal disease caused by Fusarium oxysporum) (Ammar and M.A.El-Naggar, 2011; Johnson et al., 2013). Unfortunately, fundamental molecular tools and genomic resources to enable the discovery of novel solutions to cure or prevent these threats are still lacking. In most crops, available transformation and tissue regeneration protocols have been instrumental for understanding gene function, studying plant development, and identifying resistance genes to pests and diseases. In wheat, for example, understanding resistance mechanisms against pathogens (e.g. identification of genes eliciting defense responses) has allowed the identification of resistance genes and designing preventive strategies against pathogen infection. Without this basic knowledge, any attempt to find radical solutions to protect and improve date palm production will be severely restricted.

In date palm, establishing molecular tools has been challenging, essentially because of its long generation time, lack of a transformation protocol, and lack of ultra-high quality and well-annotated reference genomes. Under optimal conditions, date palms begin to bear fruits 4 to 5 years after planting and reach full yield potential after 10 to 15 years of cultivation. In addition, though date palms can be grown from seed, they are highly heterozygous individuals and seed propagation results in altered characteristics of fruit maturation and quality in orchards. Instead of seeds, date palms are commercially propagated by offshoots that develop from axillary branches coming directly from the mother palm and thus are genetically identical and produce the fruit of the same quality as the mother. However, palms produce a limited number of offshoots and only in their early life (the first 10–15 years), which makes this propagation method slow and inefficient. In addition, the survival rate of offshoots is very low after separation from the parent and they often carry diseases (Johnson et al., 2013). Obtaining viable palms that produce fruits from homogenous tissue culture to maintain pure lines and establishing transformation protocols for date palm are the first steps toward contributing to increasing date palm production in the KSA.

Date palm production is becoming increasingly unstable because of pest infestations and abiotic threats. Understanding and exploiting these unique features will pave the path towards improving date palm production and generating crops with similar characteristics. The outcome will have a major input in promoting desert agriculture.

Figure 1: Illustration of the proposed research program.

This project aims to establish the molecular and biotechnological tools to greatly accelerate and improve date palm growth and sustainability – to make fast, fit palms – through the following short- and long-term objectives (Figure 1).

To feed the world, food production has to be increased by about 50 % until the year 2050. Although most developed countries can reach these aims by technological advances, many countries in dry and hot zones already chronically lack the production of enough food for their own population and depend on imports and foreign aid. Considering that harvest losses by drought, salt, heat and biotic stresses amounts to approx. 80 % of total productivity, improvement of stress tolerance is the main aim in crop improvement in the world. Since plants have colonized land, they have evolved mechanisms to respond to changing environmental conditions and settle in extreme habitats.

Although many plants lack the adaptive capability to adapt to stress conditions, the ability of a variety of plants to adapt to stress conditions appears to depend on the association with rhizosphere microbes, raising a number of questions: Can all plants improve stress tolerance when associated with their appropriate rhizosphere microbial partners? What distinguishes the rhizosphere microbes and plants that are adapted to extreme environmental conditions from those living in temperature zones? Did we miss to identify the right rhizosphere partners for a given plant or crop species?

Using latest genomics, transcriptomics and metabolomics methods, a freely accessible molecular database on rhizosphere microbial genomes and their gene functions will be created. By bioinformatic and functional analysis of the isolated microbes, new metabolic pathways will be identified and analysed for their use in medicine, chemical and synthetic engineering.

By functional analysis on the desert and crop host plants, the potential of the rhizosphere microbes to enhance plant stress tolerance will be established. This knowledge should lay the ground for many applications and last not least the ability to re-establish agriculture in arid regions and thereby help to secure future world food production.