Kayla M. Clouse

Sinorhizobium meliloti is a nitrogen-fixing soil bacterium that forms a facultative mutualism with its host alfalfa. S. meliloti strains exhibit diverse colony morphologies on solid culture media that span a continuum from dry to mucoid. Studies on how this trait affects symbiosis rely on mutations in exopolysaccharide II production genes; however, whether natural variation in morphology confers a selective advantage on rhizobia in their natural habitats remains unknown. Here, we used 90 mucoid and 27 dry natural isolates to test whether colony morphology associates with rhizobial fitness in the soil and in the host, or with the nitrogen-fixation benefits they provide to the plant. Colony morphologies were widely distributed across a phylogenetic tree, suggesting that morphological shifts occurred repeatedly and no single genetic variant was strongly associated with this trait. We inoculated soil mesocosms and plants with a mixture of dry and mucoid bacteria. We observed that dry rhizobia have higher fitness, particularly at 22°C and 32°C, but not under cold or drought conditions, independent of the initial rhizobial load. Conversely, mucoid bacteria have a modestly higher relative fitness in host nodules, and single inoculations showed that they tend to confer greater benefits to all three alfalfa varieties. Over time, we also observed rare, repeated conversion from mucoid to dry morphologies in soil and host plants. Taken together, our study reveals that morphological variation within a species in a single agricultural field is important for bacterial fitness in the soil and can have cascading effects on the rhizobia’s plant benefits.

Here, we present the genome sequence of Azospirillum brasilense JM 6A2 (DSM 1858), which was isolated from maize roots in Ecuador. This genome provides a resource for studying the genetic basis of nitrogen fixation and phytohormone synthesis in this agriculturally important species.

Here, we present the genome sequence of Azospirillum argentinense A2 (DSM 2297), which was previously identified as Azospirillum brasilense A2. The availability of this genome supports comparative genomic analyses and provides further species-level resolution within the genus Azospirillum .

Legumes recruit rhizobial bacteria from the soil to fix nitrogen in root nodules. The legume-rhizobia symbiosis is an early example of humans using microbes to improve crop yields. Rhizobia/microbe-based bioinoculant products often perform inconsistently in the field, across locations, and years. Rather than engineering a one-size-fits-all inoculant, identifying crop varieties that select for and reward beneficial bacteria within each field's diverse microbial community could eliminate the need for repeated inoculant applications as beneficial microbial populations increase over time. Although legume crops have not been explicitly bred to recruit and enrich beneficial rhizobia, the model legume Medicago truncatula can selectively enrich beneficial strains. Here, we investigated whether its perennial relative, Medicago sativa (alfalfa), a globally important forage crop, also has this ability. To test this, we first isolated and sequenced a collection of 117 Sinorhizobium meliloti strains from nodules of three alfalfa varieties in a field trial. Despite being isolated from nodules less than three meters apart, we found high intraspecific genetic diversity in both single-nucleotide polymorphisms and gene presence-absence, with little phylogenetic clustering by source variety. Single-strain inoculations in a nitrogen-free greenhouse experiment revealed substantial variation in nitrogen-fixation ability across strains, with the best-performing strains differing by alfalfa variety. When varieties were inoculated with a mix of all strains, no variety accumulated as much biomass as with the best single strain for that variety, indicating a lack of ability to select only the best strain when given a choice. To confirm, we evaluated relative strain fitness in nodules and found that two of the three varieties weakly enriched for beneficial strains. Our results suggest that alfalfa varieties ability to enrich beneficial rhizobial populations is a variable, breedable trait, opening the door to developing varieties optimized to enrich these populations. Ultimately, breeding hosts to enhance mutualism could improve the reliability and sustainability of field nitrogen fixation.

Heterosis, or hybrid vigor, refers to the phenotypic superiority of hybrids relative to their parental inbred lines. Recent work showed that manipulation of the soil microbial community consistently altered heterosis, but the direction of the effect was dependent on microbiome composition, environment, or both. Abiotic factors such as temperature, water availability, and soil nutrients are known modifiers of heterosis expression; however, whether interactions between the soil microbial community and abiotic properties affect heterosis is largely unknown. To further understand how microbes influence heterosis, we characterized variation in maize heterosis when grown in soil inocula derived from historical maize farms or prairies. Although we did not observe consistent differences in heterosis among plants grown in these inocula, our observations affirm that microbial effects on heterosis are likely specific to the local microbial community. The introduction of a nutrient amendment resulted in greater heterosis in the presence of an agricultural soil inoculum than in the presence of a prairie soil inoculum. In addition, the interaction between soil inoculum and nutrient treatment structured bacterial and fungal community composition in the root endosphere. Root bacterial diversity was also significantly higher under nutrient-limited conditions. These results suggest that the contributions of genotype-by-environment interactions to heterosis are dependent on microbial context. They also provide direct evidence for the interactive effect of the soil microbial community and abiotic environment on heterosis and suggest that consideration of the soil microbial community may be helpful for breeding hybrid maize varieties for high performance in diverse environmental contexts. [ ] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

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. Significance Almost all grain crops grown on commercial farms are hybrid cultivars because these hybrid plants are reliably healthier, larger, and more productive than their inbred parent lines. The widespread and valuable phenomenon of hybrid superiority is called heterosis. Despite over a century of intensive research into heterosis, it is unclear how or why hybrid genomes give rise to superior phenotypes. Most hypotheses and research thus far have focused on genetic and physiological mechanisms of heterosis. In contrast, this article presents evidence for a microbe-driven mechanism of heterosis, whereby the activity of live soil microbes affects the expression of heterosis. This finding will open lines of research that could advance our understanding of heterosis.