Microbe-dependent heterosis in maize.

Hybrids account for nearly all commercially planted varieties of maize and many other crop plants because crosses between inbred lines of these species produce first-generation [F1] offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research. The leading hypotheses-which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)-have been able to explain some but not all of the observed patterns of heterosis. Abiotic stressors are known to impact the expression of heterosis; however, the potential role of microbes in heterosis has largely been ignored. Here, we show that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved versus live soil slurries in a growth chamber and for plants grown in steamed or fumigated versus untreated soil in the field. In a different field site, however, soil steaming increased rather than decreased heterosis, indicating that the direction of the effect depends on community composition, environment, or both. Together, our results demonstrate an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize.

Phytophthora sojae Pathotype Distribution and Fungicide Sensitivity in Michigan.

Identifying the pathotype structure of a Phytophthora sojae population is crucial for the effective management of Phytophthora stem and root rot of soybean (PRR). P. sojae has been successfully managed with major resistance genes, partial resistance, and fungicide seed treatments. However, prolonged use of resistance genes or fungicides can cause pathogen populations to adapt over time, rendering resistance genes or fungicides ineffective. A statewide survey was conducted to characterize this pathotype structure and fungicide sensitivity of P. sojae within Michigan. Soil samples were collected from 69 fields with a history of PRR and fields having consistent plant stand establishment issues. Eighty-three isolates of P. sojae were obtained, and hypocotyl inoculations were performed on 14 differential soybean cultivars, all of which carry a single Rps gene or no resistance gene. The survey identified a loss of effectiveness of Rps genes 1b, 1k, 3b, and 6, compared with a previous survey conducted in Michigan from 1993 to 1997. Three effective resistance genes were identified for P. sojae management in Michigan; Rps 3a, 3c, and 4. Additionally, the effective concentration of common seed treatment fungicides to inhibit mycelial growth by 50% (EC50) was determined. No P. sojae isolates were insensitive to the tested chemistries with mean EC50 values of 2.60 × 10-2 µg/ml for ethaboxam, 3.03 × 10-2 µg/ml for mefenoxam, 2.88 × 10-4 µg/ml for oxathiapiprolin, and 5.08 × 10-2 µg/ml for pyraclostrobin. Results suggest that while there has been a significant shift in Rps gene effectiveness, seed treatments are still effective for early season management of this disease.

The interaction between abiotic and biotic soil factors drive heterosis expression in maize.

Heterosis or hybrid vigor refers to the superior phenotypes of hybrids relative to their parental inbred lines. Recently, soil microbes were identified as an environmental driver of maize heterosis. While manipulation of the soil microbial community consistently altered heterosis, the direction of the effect appeared to be dependent on the microbiome composition, environment, or both. Abiotic factors are well-known modifiers of heterosis expression, however, how the interactive effects between the soil microbial community and abiotic factors contribute to heterosis are poorly understood. To disentangle the proposed mechanisms by which microbes influence heterosis, we characterize the variation in heterosis expression when maize was grown in soil inocula derived from active maize farms or prairies. While we did not observe consistent differences in heterosis among plants grown in these inocula, our observations reaffirm that microbial effects on heterosis are likely specific to the local microbial community. The introduction of a nutrient amendment resulted in greater heterosis expression in the presence of an agricultural inoculum but not a prairie inoculum. We also observed an effect of soil inocula and nutrient treatment on the composition of bacterial and fungal communities in the root endosphere. In addition, the interaction between soil and nutrient treatment significantly affected bacterial community composition, whereas fungal community composition was only marginally affected by this interaction. These results further suggest that the soil microbial community plays a role in maize heterosis expression but that the abiotic environment is likely a larger driver.

Plant Genetics as a Tool for Manipulating Crop Microbiomes: Opportunities and Challenges.

Growing human population size and the ongoing climate crisis create an urgent need for new tools for sustainable agriculture. Because microbiomes have profound effects on host health, interest in methods of manipulating agricultural microbiomes is growing rapidly. Currently, the most common method of microbiome manipulation is inoculation of beneficial organisms or engineered communities; however, these methods have been met with limited success due to the difficulty of establishment in complex farm environments. Here we propose genetic manipulation of the host plant as another avenue through which microbiomes could be manipulated. We discuss how domestication and modern breeding have shaped crop microbiomes, as well as the potential for improving plant-microbiome interactions through conventional breeding or genetic engineering. We summarize the current state of knowledge on host genetic control of plant microbiomes, as well as the key challenges that remain.