Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping

Plants maintain microbial associations whose functions remain largely unknown. For the past 15 y, we have planted the annual postfire tobacco Nicotiana attenuata into an experimental field plot in the plant’s native habitat, and for the last 8 y the number of plants dying from a sudden wilt disease has increased, leading to crop failure. Inadvertently we had recapitulated the common agricultural dilemma of pathogen buildup associated with continuous cropping for this native plant. Plants suffered sudden tissue collapse and black roots, symptoms similar to a Fusarium–Alternaria disease complex, recently characterized in a nearby native population and developed into an in vitro pathosystem for N. attenuata. With this in vitro disease system, different protection strategies (fungicide and inoculations with native root-associated bacterial and fungal isolates), together with a biochar soil amendment, were tested further in the field. A field trial with more than 900 plants in two field plots revealed that inoculation with a mixture of native bacterial isolates significantly reduced disease incidence and mortality in the infected field plot without influencing growth, herbivore resistance, or 32 defense and signaling metabolites known to mediate resistance against native herbivores. Tests in a subsequent year revealed that a core consortium of five bacteria was essential for disease reduction. This consortium, but not individual members of the root-associated bacteria community which this plant normally recruits during germination from native seed banks, provides enduring resistance against fungal diseases, demonstrating that native plants develop opportunistic mutualisms with prokaryotes that solve context-dependent ecological problems.Eukaryotes maintain many complex relationships with the microbes they host, which can be so abundant and diverse that they frequently are considered a eukaryote’s second genome. The complex relationships mediated by microbial associates are being revealed rapidly, thanks to the advances in sequencing, microbial culturing techniques, and the reconstitution of associated microbial communities in gnotobiotic systems (1, 2), even if some of these putative functional roles may need to be evaluated more critically (3).When plants germinate from their seed banks, they typically acquire a selection of the diverse fungi and bacteria that exist in native soils, and a subset of this community becomes root-associated. The best characterized are the bacterial microbiomes of Arabidopsis thaliana. Approximately half of the bacterial community in the plant root is representative of the soil flora; the remainder is a conserved core consisting of a smaller number of bacterial lineages from three phyla: Actinobacteria, Proteobacteria, and Bacteroidetes (2, 4). Because these bacterial communities occur in nondiseased plants, they are thought to represent commensalistic or possibly mutualistic associations.Root-associated microbes could benefit plants in many ways, and a recent review (5) highlighted the parallel functional roles of the microbiomes of the human gut and those of plant roots. The best-characterized beneficial functions for plants are (i) the plant growth-promoting rhizobacteria (PGPR), which promote growth by a variety of direct and indirect means that include increasing nutrient availability, interfering with ethylene (ET) signaling, and preventing diseases (6), and (ii) the bacteria that elicit induced systemic resistance (ISR) (7) by activating jasmonic acid (JA) and ET signaling (8). PGPR and ISR have been studied in a variety of cultivated and model plants, usually with model microbes (5), but little is known about their ecological context or whether they increase the growth and fitness of native plants. Whether PGPR and ISR functions occur among the well-characterized root-associated bacterial communities of Arabidopsis, either collectively or individually, also remains unknown.The well-described agricultural phenomenon of disease-suppressive soils that harbor microbiomes that suppress particular soil-borne pathogens (9) illustrates the complexity of the dynamics involved. Native soils have a certain degree of pathogen-suppressive ability, frequently seen when a crop is grown continuously in a soil, suffers an outbreak of a disease, and subsequently becomes resistant to the disease (5). Perhaps the mechanisms involved are best understood in a root disease of wheat caused by Gaeumannomyces graminis var Tritici infections, known as “take-all” disease. After many years of continuous wheat cropping with several disease outbreaks, the disease suddenly wanes, apparently because of the build-up of antagonistic Pseudomonas spp. (9). Whether any of these interactions also occur in native plants remains unknown.Nicotiana attenuata, a native annual tobacco of North America, germinates from long-lived seed banks to grow in the immediate postfire environment (10). When N. attenuata seeds germinate from their seed banks, they acquire a root-associated microbiome from their native soils which has been characterized by pyrosequencing and culture-dependent approaches (11–14). The composition of the root-associated microbiome is not influenced by a plant’s ability to elicit JA signaling (14), but ET signaling, as mediated by the ability both to produce and to perceive ET, plays a decisive role in shaping the “immigration policy” for the root-associated microbiome (12). A certain Bacillus strain, B55, was isolated from the roots of an ET-insensitive N. attenuata plant (35S etr-1) and was able to rescue the impaired-growth and high-mortality phenotype of ET-insensitive plants under field conditions (15). Beneficial effects were attributed to B55’s ability to reduce sulfur and produce dimethyl disulfide, which N. attenuata uses to alleviate sulfur deficiencies. This rescue provided one of the first demonstrations that the soil bacteria recruited by plants during germination can form opportunistic mutualistic relationships with their host based on the host plant’s ecological context. Here we provide a second example that involves protection against a sudden wilt disease, which accumulated in a field plot after consecutive planting of N. attenuata seedlings.