The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils

Abstract

Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina and Glycine soja, which grow in saline soils of the Yellow River Delta, China, using PacBio’s circular consensus sequencing for full-length bacterial 16S rRNA gene to obtain finer taxonomic information. The cultivated legume Glycine max was used for comparison. We identified 18 bacterial genera and 55 species in nodule samples, which mainly classified to Proteobacteria, and rhizobial genus Ensifer was the predominant group. The three legumes showed similarity in operational taxonomic unit (OTU) diversity but distinction in OTU richness, indicating that they harbor similar bacterial species with different relative contents. The results of principal coordinates analysis and ANOSIM tests indicated that G. soja and G. max have similar nodule bacterial communities, and these communities differ from that of S. cannabina. Wild legumes S. cannabina and G. soja both harbored a higher number of rhizobia, while G. max possessed more non-rhizobial bacteria. These differences could be associated with their adaptability to saline–alkali stress and revealed clues on the nodule endophytes with relative importance of culturable rhizobial symbionts.

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

“…A total of 1,528 ± 39 and 1,797 ± 246 OTUs were obtained from the clean sequences from the SDY and Ss root zones, respectively ( Supplementary Table S1), whereas only 358 ± 209 and 164 ± 10 OTUs were obtained from the nodules of wild soybean grown in these regions, respectively. We found that the barren sand root zone carried more OTUs than the fertile soil; however, our previous study identified 191 ± 13 OTUs in nodules using PacBio's circular consensus sequencing for full-length bacterial 16S rRNA (Zheng et al, 2020), similar to the 164 ± 10 OTUs obtained here. The dataset was rarefied to an even sequencing depth of 20,000 sequences and 2,423 bacterial OTUs were identified.…”

“…Based on relative abundance, the most common phyla (>0.1%) in the coastal nodule samples (nS) and Yellow River Delta nodule samples (nD), respectively, were Proteobacteria (98.458 ± 0.045 and 99.703 ± 0.002%), Actinobacteria (0.533 ± 0.340 and 0.167 ± 0.047%), Bacteroidetes (0.177 ± 0.158 and 0.037 ± 0.017%), Chloroflexi (0.123 ± 0.122 and 0.047 ± 0.009%), Acidobacteria (0.113 ± 0.092 and 0.043 ± 0.012%), and Gemmatimonadetes (0.117 ± 0.095 and 0.043 ± 0.009%), indicating that nS samples displayed a higher diversity and proportion than nD samples. As predicted, the most prominent Proteobacteria were Sinorhizobium/Ensifer (97.330 ± 1.701 and 98.661 ± 0.471%); however, the proportion differed (85.67 ± 6.29%) from PacBio's circular consensus sequencing for full-length bacterial 16S rRNA gene in nD samples (Zheng et al, 2020).…”

“…Conversely, only one Bacteroidetes genus Dyadobacter (five isolates) was isolated from nS samples. Our previous study at the species level identified four genera with high relative abundance: Enterobacter, Chryseobacterium, Stenotrophomonas, and Flavobacterium (Zheng et al, 2020); however, only Enterobacter spp. were isolated in this study, which have been reported to be microsymbionts of G. soja (Zhao et al, 2014).…”

Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products

“…Nodule microbiome analysis of rhizobial populations shows the Bradyrhizobium genus as the predominant mung bean micro-symbiont in Brazilian tropical soils independent from both plant genotypes and whether soil samples present (or do not) a history of mung bean cultivation. A predominance of a rhizobial genus in legume nodules is commonly reported ( Sharaf et al, 2019 ; Hakim et al, 2020 ; Rocha et al, 2020 ; Zheng et al, 2020 ). Isolation of diazotrophic strains from mung bean nodules cultivated in different soils worldwide have shown a predominance of Bradyrhizobium strains ( Yang et al, 2008 ; Zhang et al, 2008 ; Appunu et al, 2009 ; Risal et al, 2012 ).…”

Diversity of microbial communities and soil nutrients in sugarcane rhizosphere soil under water soluble fertilizer

“…A NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, Massachusetts, USA) was used to assess the quality and concentration of soil DNA. A sequencing library was prepared using primers sets 27F/1492R [ 22 , 23 ] and ITS9munngs/ITS4ngsUni [ 24 ] to amplify the 16S rRNA gene and ITS. PCR conditions were 95°C for 5 min, followed by 30 cycles of 95°C for 30 s, 55°C for 30 s, and 72°C for 1min 30 s, with a final extension at 72°C for 7 min (GeneAmp 9700, ABI, California CA, USA).…”