Background Soybean ( Glycine max ) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is more sustainable than most other cropping systems. Diazotrophs inhabiting root nodules provide soybean with nitrogen required for growth. Despite the knowledge of culturable Bradyrhizobium spp. and how they can differ across cultivars, less is known about the overall bacterial community (bacteriome) diversity within nodules, in situ. This variability could have large functional ramifications for the long-standing scientific dogma related to the plant-bacteriome interaction. Water availability also impacts soybean, in part, as a result of water-deficit sensitive nodule diazotrophs. There is a dearth of information on the effects of cultivar and water status on in situ rhizobia and non-rhizobia populations of nodule microbiomes. Therefore, soybean nodule microbiomes, using 16S rRNA and nifH genes, were sampled from nine cultivars treated with different field water regimes. It was hypothesized that the nodule bacteriome, composition, and function among rhizobia and non-rhizobia would differ in response to cultivar and soil water status. Results 16S rRNA and nifH showed dominance by Bradyrhizobiaceae , but a large diversity was observed across phylogenetic groups with < 1% and up to 45% relative abundance in cultivars. Other groups primarily included Pseudomonadaceae and Enterobacteriaceae . Thus, nodule bacteriomes were not only dominated by rhizobia, but also described by high variability and partly dependent on cultivar and water status. Consequently, the function of the nodule bacteriomes differed, especially due to cultivar. Amino acid profiling within nodules, for example, described functional changes due to both cultivar and water status. Conclusions Overall, these results reveal previously undescribed richness and functional changes in Bradyrhizobiaceae and non-rhizobia within the soybean nodule microbiome. Though the exact role of these atypical bacteria and relative variations in Bradyrhizobium spp. is not clear, there is potential for exploitation of these novel findings of microbiome diversity and function. This diversity needs consideration as part of bacterial-inclusive breeding of soybean to improve traits, such as yield and seed quality, and environmental resilience. Electronic supplementary material The online version of this article (10.1186/s40168-019-0676-8) contains supplementary material, which is available to authorized users.

Nitrogen (N) bioavailability is a primary limiting nutrient for crop and feedstock productivity. Associative nitrogen fixation (ANF) by diazotrophic bacteria in root-zone soil microbial communities have been shown to provide significant amounts of N to some tropical grasses, but this potential in switchgrass, a warm-season, temperate, US native, perennial tallgrass has not been widely studied. 'Alamo' and 'Dacotah' are cultivars of switchgrass, adapted to the southern and northern regions of the United States, respectively, and offer an opportunity to better describe this plant-bacterial association. The nitrogenase enzyme activity, microbial communities, and amino acid profiles in the root-zones of the two ecotypes were studied at three different plant growth stages. Differences in the nitrogenase enzyme activity and free soluble amino acid profiles indicated the potential for greater nitrogen fixation in the high productivity Alamo compared with the lower productivity Dacotah. Changes in the amino acid profiles and microbial community structure (rRNA genes) of the root-zone suggest different plant-bacterial interactions can help to explain differences in nitrogenase activity. PICRUSt analysis revealed functional differences, especially nitrogen metabolism, that supported ecotype differences in root-zone nitrogenase enzyme activity. It is thought that the greater productivity of Alamo increased the belowground flow of carbon into roots and root-zone habitats, which in turn support the high energy demands needed to support nitrogen fixation. Further research is thus needed to understand plant ecotype and cultivar trait differences that can be used to breed or genetically modify crop plants to support root-zone associations with diazotrophs.

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The biodegradable film application can escape from plastic environmental pollution. This experiments studied the effect of biodegradable mulch film on the soil microbial community using fatty acid methyl ester method in soybean production field. The soil NO 3 -N content in polyethylene mulch film (PE) soil was significantly higher than biodegradable mulch film soil (p < 0.05). The soil microbial community of Gram negative bacteria showed significantly higher in biodegradable mulch film soil than PE mulch film soil (p < 0.05). In addition, biodegradable mulch film soil had significantly low ratio of cy17:0 to 16:1ω7c and cy19:0 to 18:1ω7c compared with those of PE mulch film soil (p < 0.05), indicating that microbial stress decreased. The ratio of cy17:0 to 16:1ω7c and cy19:0 to 18:1ω7c should be considered as a potential responsible factor for the obvious differentiation that was observed between the biodegradable mulch film soil and PE mulch film soil in a upland field. The results of this experimentation show the potential of using biodegradable mulch film in place of PE.Key words: Microbial community, Biodegradable film, Polyethylene film, Fatty acid methyl ester (FAME) Ratio of cy17:0 to 16:1ω7c and cy19:0 to 18:1ω7c of different mulch film soils for soybean cultivation. Means by the same letter within a column are not significantly different at 0.05 probability level according to Tukey's studentized range test. Bars represent one standard deviation of the mean.