Abstract
Rhizosphere microorganisms play important roles in plant health and nutrition, and interactions among plants and microorganisms are important for establishment of root microbiomes. As yet, plant-microbe and microbe-microbe interactions in the rhizosphere remain largely mysterious. In this study, rhizosphere fungal community structure was first studied in a field experiment with two soybean cultivars contrasting in nodulation grown in two rhizobium inoculation treatments. Following this, recombinant inbred lines (RILs) contrasting in markers across three QTLs for biological nitrogen fixation (BNF) were evaluated for effects of genotype and rhizobium inoculation to the rhizosphere fungal community as assessed using ITS1 amplicon sequencing. The soybean plants tested herein not only hosted rhizosphere fungal communities that were distinct from bulk soils, but also specifically recruited and enriched Cladosporium from bulk soils. The resulting rhizosphere fungal communities varied among soybean genotypes, as well as, between rhizobium inoculation treatments. Besides, Cladosporium were mostly enriched in the rhizospheres of soybean genotypes carrying two or three favorable BNF QTLs, suggesting a close association between soybean traits associated with nodulation and those affecting the rhizosphere fungal community. This inference was bolstered by the observation that introduction of exogenous rhizobia significantly altered rhizosphere fungal communities to the point that these communities could be distinguished based on the combination of soybean genotype and whether exogenous rhizobia was applied. Interestingly, grouping of host plants by BNF QTLs also distinguished fungal community responses to rhizobium inoculation. Taken together, these results reveal that complex cross-kingdom interactions exist among host plants, symbiotic N2 fixing bacteria and fungal communities in the soybean rhizosphere.
Highlights
Since colonizing land 450 million years ago, plants have co-evolved with associated microbes (Rosenberg and Zilber-Rosenberg, 2016)
Our results demonstrate that soybean rhizosphere fungal community responses to rhizobium inoculation are strongly influenced by genotypic differences at a few key markers associated with N2 fixation
We demonstrated that soybean plants could recruit certain fungi from bulk soils, which led to distinctive fungal communities in soybean rhizospheres
Summary
Since colonizing land 450 million years ago, plants have co-evolved with associated microbes (Rosenberg and Zilber-Rosenberg, 2016). Roots of soil-grown plants function in mineral nutrient uptake and provide sites for association with soil-inhabiting microbes in the rhizosphere (Hacquard et al, 2015). Rhizobium Drives Soybean and Fungal Interactions while establishing distinct plant microbiomes that play important roles in both the phyllosphere and rhizosphere (Agler et al, 2016). Available research suggests that the establishment of plant root microbiomes largely depends on root exudates, and is strongly influenced by preferences for specific sets of microbial carbohydrates (Hu et al, 2018; Stringlis et al, 2018; Zhalnina et al, 2018; Huang et al, 2019). There is little information available on specific interactions between prokaryotic and eukaryotic microorganisms responsible for the establishment of plant-associated microbiomes (Hassani et al, 2018)
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