Feeding nutrition-dense food to future world populations presents agriculture with enormous challenges as estimates indicate that crop production must as much as double. Crop production cannot be increased to meet this challenge simply by increasing land acreage or using past agricultural intensification methods. Food production doubled in the past through substantial use of synthetic fertilizer, pesticides, and irrigation, all at significant environmental cost. Future production of nutrition-dense food will require next-generation crop production systems with decreased reliance on synthetic fertilizer and pesticide. Here, we present three case studies detailing the development of cover crops and plant-beneficial microbes for sustainable, next-generation small grain, tomato, and oilseed rape production systems. Cover crops imparted weed and pathogen control and decreased soil erosion and loss of soil nitrogen, phosphorus and carbon, while plant-beneficial microbes provided disease control and phosphorus fertility. However, yield in these next-generation crop production systems at best approximated that associated with current production systems. We argue here that to substantially increase agricultural productivity, new crop germplasm needs to be developed with enhanced nutritional content and enhanced tolerance to abiotic and biotic stress. This will require using all available technologies, including intensified genetic engineering tools, in the next-generation cropping systems.

The agricultural community is confronted with dual challenges; increasing production of nutritionally dense food and decreasing the impacts of these crop production systems on the land, water, and climate. Control of plant pathogens will figure prominently in meeting these challenges as plant diseases cause significant yield and economic losses to crops responsible for feeding a large portion of the world population. New approaches and technologies to enhance sustainability of crop production systems and, importantly, plant disease control need to be developed and adopted. By leveraging advanced geoinformatic techniques, advances in computing and sensing infrastructure (e.g., cloud-based, big data-driven applications) will aid in the monitoring and management of pesticides and biologicals, such as cover crops and beneficial microbes, to reduce the impact of plant disease control and cropping systems on the environment. This includes geospatial tools being developed to aid the farmer in managing cropping system and disease management strategies that are more sustainable but increasingly complex. Geoinformatics and cloud-based, big data-driven applications are also being enlisted to speed up crop germplasm improvement; crop germplasm that has enhanced tolerance to pathogens and abiotic stress and is in tune with different cropping systems and environmental conditions is needed. Finally, advanced geoinformatic techniques and advances in computing infrastructure allow a more collaborative framework amongst scientists, policymakers, and the agricultural community to speed the development, transfer, and adoption of these sustainable technologies.

There is a pressing need for redesigning agriculture to achieve sustainability and for utilizing modern genetic tools, including genetic engineering, to add nutritional value to crops for the benefit of the diverse human population. Collectively, plant foods contain most minerals, macronutrients (calories), and micronutrients essential for human nutrition. These plant foods also contain a range of bioactive compounds that can play important roles in the prevention of chronic diseases including heart disease, cancer, stroke, diabetes, Alzheimer's, cataracts, and age-related functional decline. However, these bioactive nutrients are often present at marginal concentrations in edible plant tissues in regard to human nutrition/prevention of disease. The quantity of these nutrients in edible plant tissues is primarily dependent on crop genetics and regulated by complex and overlapping mechanisms in response to developmental and environmental cues. Environmental cues are naturally occurring—temperature, light intensity, and other stressors, or result from crop production system components—fertilizer, tillage operations, etc. One strategy for sustainable, next-generation crop development is to design cropping systems that have minimal or lesser impact on the environment and to use genetic approaches to enhance crop nutritional content. This strategy is appealing since crop genetics is the primary driver of plant nutrient content and because purely managing crop production fields to optimize crop nutrient content is extremely challenging if not impossible. As an example we present the development of a next-generation sustainable tomato production system with beneficial impacts on tomato physiology and nutritional quality of the tomato fruit. Our analysis of the metabolomes of tomato cultivars in this and other cropping systems highlights the need for robust cultivars that consistently express nutritional and other desirable traits across cropping systems and under differing environmental conditions.

The root nodules are a unique environment formed on legume roots through a highly specific symbiotic relationship between leguminous plants and nodule-inducing bacteria. Previously, Rhizobia were presumed to be the only group of bacteria residing within nodules. However, recent studies discovered diverse groups of bacteria within the legume nodules. In this report soybean nodule-associated bacteria were studied in an effort to identify beneficial bacteria for plant disease control and growth promotion. Analysis of surface-sterilized single nodules showed bacterial diversity of the nodule microbiome. Five hundred non-rhizobial colonies from 10 nodules, 50 colonies per nodule, were tested individually against the tomato wilt causing bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) for inhibition of pathogen growth. From the initial screening, 54 isolates were selected based on significant growth inhibition of Cmm. These isolates were further tested in vitro on another bacterial pathogen Pseudomonas syringae pv. tomato (Pst) and two fungal pathogens Rhizoctonia solani and Sclerotinia sclerotiorum. Bacterial metabolites were extracted from 15 selected isolates with ethanol and tested against pathogen Cmm and Pst. These isolates were identified by using MALDI-TOF mass spectrometry and 16S rRNA gene sequencing. Pseudomonas spp. were the dominant soybean nodule-associated non-rhizobial bacterial group. Several isolates imparted significant protection against pathogens and/or plant growth promotion on tomato seedlings. The most promising nodule-associated bacterial isolate that suppressed both Cmm and Pst in vitro and Pst in tomato seedlings was identified as a Proteus species. Isolation and identification of beneficial nodule-associated bacteria established the foundation for further exploration of potential nodule-associated bacteria for plant protection and growth promotion.