Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil

Abstract

Soil salinization limits crop growth and yield in agro-ecosystems worldwide by reducing soil health and altering the structure of microbial communities. Salt-tolerant plant growthpromoting rhizobacteria (PGPR) alleviate plant salinity stress. Wild soybean (Glycine soja Sieb. and Zucc.) is unique in agricultural ecosystems owing to its ability to grow in salinealkali soils and fix atmospheric nitrogen via symbiotic interactions with diverse soil microbes. However, this rhizosphere microbiome and the nodule endosymbionts have not been investigated to identify PGPR. In this study, we investigated the structural and functional rhizosphere microbial communities in saline-alkali soil from the Yellow River Delta and coastal soil in China, as well as wild soybean root nodule endosymbionts. To reveal the composition of the microbial ecosystem, we performed 16S rRNA and nifH gene amplicon sequencing on root nodules and root zones under different environmental conditions. In addition, we used culture-independent methods to examine the root bacterial microbiome of wild soybean. For functional characterization of individual members of the microbiome and their impact on plant growth, we inoculated isolates from the root microbiome with wild soybean and observed nodulation. Sinorhizobium/Ensifer accounted for 97% of the root nodule microbiome, with other enriched members belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes; the genera Sphingomonas, Microbacterium, Arthrobacter, Nocardioides, Streptomyces, Flavobacterium, Flavisolibacter, and Pseudomonas; and the family Enterobacteriaceae. Compared to saline-alkali soil from the Yellow River Delta, coastal soil was highly enriched for soybean nodules and displayed significant differences in the abundance and diversity of β-proteobacteria, δ-proteobacteria, Actinobacteria, and Bacteroidetes. Overall, the wild soybean root nodule microbiome was dominated by nutrient-providing Sinorhizobium/ Ensifer and was enriched for bacterial genera that may provide salt resistance. Thus, this reductionist experimental approach provides an avenue for future systematic and functional studies of the plant root microbiome.

Effect of different biochar particle sizes together with bio-organic fertilizer on rhizosphere soil microecological environment on saline–alkali land

“…More than 800 Mha of the world's agricultural land is composed of saline soil, either based on salinity (397 Mha) or sodicity (434 Mha) (FAO, 2020), whereas there is approximately 8.11 × 10 7 ha of saline-alkali soil in China, which accounts for 8%-9% of the total land area (Zhao et al, 2014). The Yellow River delta is one of the three largest river deltas in China and is becoming an important region for agricultural development (Jing et al, 2019); however, crop production is limited by high soil salinity (Yang et al, 2020), and thus far, the utilization of this saline-alkali land has not been effectively managed. The development of strategies to make use of saline-alkali land will be crucial in addressing problems of insufficient cropland and meeting the challenge of providing food security for the projected global population of 9.3 billion people by 2050 (Shabala et al, 2015).…”

All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication

“…[9,71,78]. Moreover, among the same studies, high abundances of Chloroflexi were observed in the rhizosphere of soybean, oilseed rape, and wild grassland species [9,72,78], and-together with Flavisolibacter-even in the microbial community in the nodules of wild soybean [76]. OTUs assigned to the ammonia-oxidizing archaea Candidatus Nitrososphaera [81,82] were reported from the rhizosphere of oilseed rape and maize, and Rhizobium from the endosphere of oilseed rape, wheat, and canola roots [78,79].…”

“…Gemmatimonadetes were among the four dominant phyla in the rhizosphere of lentil, pea, soybean, wheat, maize, canola, oilseed rape, artichoke, and diverse grassland species from temperate zones in Europe or the Chinese tundra [9,26,72,[76][77][78][79][80]. Several of these studies demonstrated the enrichment of Gemmatimonadetes in the rhizosphere as compared to bulk soil [78] and linked this phylum to increased biomass production or increased resistance to salt stress [76,77,80], mainly due to abundant nitrogen-fixing Gemmatimonas spp. [9,71,78].…”

Environmental factors and host genotype control foliar epiphytic microbial community of wild soybeans across China

“…Owing to complex geographic and ecological conditions, there are many genotypes of wild soybean distributed throughout China following long-term climatic and environmental selection ( Guo et al, 2012 ; Li and Wang, 2020 ). Current studies have concentrated on the microbiome of root nodules ( Yang et al, 2020 ; Zheng et al, 2020 ) and the rhizosphere ( Chang et al, 2019 ; Tian et al, 2020 ) to investigate the microbial nitrogen fixation capacity in this legume species ( Mahmud et al, 2020 ). However, little information has been reported on the importance of climate and host genotype in regulating the foliar microbiome of wild soybeans.…”