Christine Hawkes

A major challenge for humankind is to feed the increasing human population in a sustainable manner. According to UN’s development programme extreme hunger and malnutrition is a major barrier to development in many countries: 795 million people are estimated to be chronically undernourished as of 2014, often as a direct consequence of environmental degradation, drought and loss of biodiversity. The Sustainable Development Goals (SDGs) aim to end hunger and malnutrition by 2030. Improved agricultural productivity is a critical part of achieving the SDG goal 2, Zero Hunger. Currently more than one third of crop yields are lost due to abiotic and biotic stress factors, such as drought, salinity, pests and disease. To minimize this yield gap and to simultaneously reduce the environmental impact of current agricultural practices, future crop production needs to be achieved on sub-optimal soils with reduced input of fertilizers and pesticides (‘more with less’). These challenges have increased the awareness of the importance of the plant microbiome for improved agricultural practices. Plants are colonized by an astounding number of microorganisms that can have profound effects on seed germination, seedling vigour, plant growth and development, nutrition, diseases and productivity. Thus, the plants can be viewed as holobionts that benefits from its microbiome in terms of specific functions and traits. In return, plants transfer a substantial part of their photosynthetically fixed carbon directly into symbionts and into their immediate surroundings thereby supporting the microbial community and influencing its composition and activities. For the vast majority of plant-associated microorganisms, however, there is little knowledge of their specific impact on crop growth and crop resilience and the mechanisms underlying microbiome-plant interactions. Hence, a critical step in developing new microbiome-assisted approaches to quantitatively and predictably improve crop resilience management strategies is deciphering the hyperdiverse plant microbiome. In particular, we need to identify keystone microorganisms and mechanisms involved in plant growth promotion and protection against biotic and abiotic stresses. To that end, systems-based analyses combined with deep-learning and modelling are essential to decode the taxonomic diversity and functional potential of plant microbiomes. The overall aim of this multidisciplinary research program is to develop a scalable system-based strategy to harness the functional potential of plant microbiomes for improving crop resilience. More specifically, we will focus on experimental analyses and modelling of the phyllosphere microbiome of wheat (Triticum aestivum), one of the most important cereal food crops worldwide. The phyllosphere microbiome is defined here as the collective microbial communities inhabiting both the leaf surface as well as the internal leaf tissue. We will zoom in on the microbiome of flag leaves of wheat, as the flag leaf is a major determinant (up to 45%) of wheat yield. To do this, we combine renowned academic expertise in microbiology, chemistry, DNA and RNA sequencing, bioinformatics, machine-learning and modelling with company support in plant breeding and agronomy to deliver novel approaches and technologies.

Panicum virgatum (switchgrass) is a promising biofuel species based on its broad geographic range, perennial life history, high biomass production, and tissue quality. These characteristics also make P. virgatum potentially suitable for cultivation on marginal lands with low inputs. Recent work suggests that fungal symbionts of P. virgatum are an important controller of physiology, with large impacts on plant size and nutrient access that have the potential to affect carbon and water cycling as well as growth and survival on marginal lands. We will address how root fungal symbionts interact to affect plant performance and biogeochemical cycling. Specifically, we will quantify the role of individual symbionts in the plant carbon and nutrient economy, determine whether and how the plant maintains beneficial symbionts when colonized by fungi with differential benefits, and examine how scaling up to realistic communities of root fungi that allow for fungal interactions may alter these processes.

Despite the recent inclusion of new microbial mechanisms in ecosystem models, our ability to predict existing carbon pools remains limited and consequently reduces our confidence in projections of future carbon stocks. Past efforts have been focused on microbial temperature responses, but moisture may be a more important constraint on microbial activity. Here, we propose that an understanding of soil microbial moisture responses is required to improve ecosystem carbon models. Specifically, we address four key questions: (1) What is the shape of the moisture response function for microbial physiological processes across ecosystems?, (2) How does drought alter moisture response curves across ecosystems?, (3) What are the microbial mechanisms underpinning moisture responses and acclimatization?, and (4) How does the incorporation of soil moisture responses and legacies affect soil carbon model dynamics? In order to build a robust predictive framework for soil microbial moisture functions, we will leverage the existing DroughtNet RCN, with 144 sites in 35 countries worldwide that have implemented coordinated experiments with ambient precipitation and drought treatments. Soils from ambient and drought treatments will be exposed to a full range of soil water potentials to quantify moisture response functions for three key microbial processes: soil respiration, enzyme activities, microbial biomass. Underlying microbial mechanisms will be examined by characterizing physiological traits and tolerances at individual and community levels. We will scale results to the ecosystem level by incorporating moisture response functions and acclimatization potential into conventional and microbially explicit models of soil carbon cycling.

All plants, including crops, contain a fungal microbiome. Plant fungal interactions can impact the growth of individual plants and contribute to nutrient cycling across entire ecosystems. Climate change is expected to increase the severity and frequency of droughts and these events will be a major impediment to global food security. Global climate models predict global wheat production will decrease by 1.9% by 2050. These changing climatic conditions are expected to increase the instances of certain wheat pathogens due to drought and high temperatures. In addition, abiotic stress is likely to influence the outcome of fungal microbiome-pathogen interactions. With increasing frequency and severity of extreme weather events that will threaten food security, it is essential to understand plant response to stress and how that is affected by their microbial community, including the underlying molecular mechanisms of microbial interactions that can improve stress tolerance. The studies proposed here will investigate the underlying mechanisms impacting plant response to stress and, from this, we can find which genes in fungal communities can aid or abet crop response to stress and pave the way for new microbial genetic screens and manipulations to take place.

More than a third of crop yields are currently lost due to abiotic and biotic stressors such as drought, pests, and disease. These stressors are expected to worsen in a warmer, drier future, resulting in crop yields further declining ~25%; however, breeding is only expected to rescue 7-15% of that loss [1]. The plant microbiome is a new avenue of plant management that may help fill this gap. All plants have fungi living inside their leaves (“foliar fungal endophytes”). This is an ancient and intimate relationship in which the fungi affect plant physiology, biotic and abiotic stress tolerance, and productivity. For example, some foliar fungi prevent or delay onset of major yield-limiting diseases caused by pathogens such as Fusarium head blight [2]. Foliar endophytes also reduce plant water loss by up to half and delay wilting by several weeks [3, 4]. Endophyte effects on plants occur via diverse genes and metabolites, including genes involved in stress responses and plant defense [5]. Genes and metabolites also predict how interactions in fungal consortia affect host stress responses, which is important for developing field inoculations [6]. Because newly emergent leaves lack fungi, endophytes are also an attractive target for manipulation (particularly compared to soils, where competition with the existing microbial community inhibits microbial additives). We propose to address the role of endophytic “mycobiomes” in stress tolerance of five North Carolina food, fiber, and fuel crops (corn, hemp, soybean, switchgrass, wheat), and to develop tools that can push this field beyond its current limits. Our major objectives (Fig. 1) are to: 1. Identify key microbiome scales to optimally manage endophytes 2. Determine fungal mechanisms via greenhouse tests, modeling, and genetic engineering 3. Build tools for field detection of endophytes 4. Understand the regulatory environment and engage diverse stakeholders Results of these objectives will allow us to make significant progress in both understanding the basic biology of plant-fungal interactions and managing those interactions in real-world settings. Our extension efforts will also bring these ideas to the broader community. Finally, we will also be well positioned to pursue several future research endeavors supported by federal granting agencies.