Contemporary issues in agriculture and natural resource management (AGNR) span a wide spectrum of challenges and scales—from global climate change to resiliency in national and regional food systems to the sustainability of livelihoods of small-holder farmers—all of which may be characterized as complex problems. With rapid development of tools and technologies over the previous half century (e.g., computer simulation), a plethora of disciplines have developed methods to address individual components of these multifaceted, complex problems, oftentimes neglecting unintended consequences to other systems. A systems thinking approach is needed to (1) address these contemporary AGNR issues given their multi- and interdisciplinary aspects; (2) utilize a holistic perspective to accommodate all of the elements of the problem; and (3) include qualitative and quantitative techniques to incorporate “soft” and “hard” elements into the analyses. System dynamics (SD) methodology is uniquely suited to investigate AGNR given their inherently complex behaviors. In this paper, we review applications of SD to AGNR and discuss the potential contributions and roles of SD in addressing emergent problems of the 21st century. We identified numerous SD cases applied to water, soil, food systems, and smallholder issues. More importantly, several case studies are shown illustrating the tradeoffs between short-term and long-term strategies and the pitfalls of relying on quick fixes to AGNR problems (known as “fixes that backfire” and “shifting the burden”, well-known, commonly occurring, systemic structures—or archetypes—observed across numerous management situations [Senge, P.M. The Fifth Discipline, 1st ed.; Doubleday: New York, NY, USA, 1990.]). We conclude that common attempts to alleviate AGNR problems, across continents and regardless of the type of resources involved, have suffered from reliance on short-term management strategies. To effectively address AGNR problems, longer-term thinking and strategies aimed at fundamental solutions will be needed to better identify and minimize the often delayed, and unintended, consequences arising from feedback between management interventions and AGNR systems.

The presence of the fungal endophyte Neotyphodium coenophialum in tall fescue (Festuca arundinacea) confers resistance to some plant-parasitic nematodes but also results in the production of ergot alkaloids. Recently, new strains of N. coenophialum have been isolated from wild tall fescue and artificially inoculated into elite tall fescue cultivars. These strains produce low to nil levels of ergot alkaloids and are referred to as non-ergot strains. Our objective was to determine whether non-ergot strains of the endophyte confer the same level of resistance to Pratylenchus spp. as the endemic strain in tall fescue. In a glasshouse experiment, nematode resistance was compared in two fescue cultivars (Jesup and Georgia 5) infected with either the endemic strain (E+), or two non-ergot strains, AR542 and AR584. An additional non-ergot strain, AR514, was tested only in cv. Jesup. Cultivars Georgia 5 and Jesup without endophytes (E−) were used as controls. The endophtye status of the plants was confirmed and then three plants per cultivar/endophyte combination were transplanted into 10 cm square pots. The pots were inoculated with a mixed culture of Pratylenchus zeae and P. scribneri in the first trial and a pure culture of P. scribneri in the second trial of the experiment. After 8 weeks, the number of nematodes within the roots from each pot was determined. Numbers of Pratylenchus spp. in either cv. Georgia 5 or cv. Jesup containing the non-ergot strain AR542 were not different from numbers in E− plants. AR514 also did not confer resistance to the nematodes in cv. Jesup. By contrast, the non-ergot strain AR584 appears to confer resistance to Pratylenchus spp. in cv. Georgia 5, but not in cv. Jesup; however, the level of resistance in cv. Georgia 5 was less than the resistance conferred by the endemic endophyte. Genetic differences between the two tall fescue cultivars may affect growth of the endophyte or production of a nematode toxin or deterrent by the endophyte. As only a small subset of endophyte strains has been tested, we are screening additional non-ergot strains for resistance to P. scribneri.